BioC 2.14: CHECK report for flowWorkspace on morelia

Package: flowWorkspace

Version: 3.10.09

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowWorkspace_3.10.09.tar.gz

StartedAt: 2014-10-07 22:50:50 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:57:11 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 381.0 seconds

RetCode: 0

Status:  OK

CheckDir: flowWorkspace.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch flowWorkspace_3.10.09.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/flowWorkspace.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowWorkspace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘flowWorkspace’ version ‘3.10.09’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowWorkspace’ can be installed ... [214s/216s] OK
* checking installed package size ... NOTE
  installed size is 18.9Mb
  sub-directories of 1Mb or more:
    lib     7.5Mb
    libs    7.7Mb
    tests   2.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graph’ ‘Biobase’ ‘gridExtra’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘IDPmisc’ ‘RBGL’ ‘graphics’ ‘hexbin’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘Rgraphviz:::getRenderPar’ ‘flowCore:::checkClass’
  ‘flowCore:::copyFlowSet’ ‘flowCore:::guid’ ‘graph:::.makeEdgeKeys’
  ‘lattice:::updateList’ ‘ncdfFlow:::.isValidSamples’
  ‘stats:::.splinefun’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.load_gs’ ‘.uuid_gen’ ‘isNegated’ ‘trimWhiteSpace’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getTransformations : <anonymous> : f: no visible binding for global
  variable ‘max_val’
.getTransformations : <anonymous> : f: no visible binding for global
  variable ‘decade’
.getTransformations : <anonymous> : f: no visible binding for global
  variable ‘min_val’
.getTransformations : <anonymous>: multiple local function definitions
  for ‘f’ with different formal arguments
* 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 portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [13s/13s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
GatingHierarchy-class 4.825  0.199   5.106
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘run-all.R’ [34s/34s]
 [34s/35s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/flowWorkspace.Rcheck/00check.log’
for details.

* installing *source* package ‘flowWorkspace’ ...
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for size_t... yes
configure: setting xml2 flags...
configure: No directory was specified for --with-xml2. Trying to find xml2 using other methods.
checking for xml2-config... /usr/bin/xml2-config
configure: No directory was specified for --with-boost. Using bundled boost.
found  bst  header sources and tar archive;using what is there.
configure: Using the following compilation and linking flags for flowWorkspace
configure:    PKG_CPPFLAGS=-I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900
configure:    PKG_LIBS=-lxml2 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GatingHierarchy.cpp -o GatingHierarchy.o
GatingHierarchy.cpp:866:11: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
        if(target>=0&&target<=boost::num_vertices(tree)-1)
           ˜˜˜˜˜˜^ ˜
GatingHierarchy.cpp:901:11: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
        if(source>=0&&source<=boost::num_vertices(tree)-1)
           ˜˜˜˜˜˜^ ˜
GatingHierarchy.cpp:957:6: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare]
        if(u>=0&&u<=boost::num_vertices(tree)-1)
           ˜^ ˜
GatingHierarchy.cpp:961:73: warning: adding 'VertexID' (aka 'unsigned long') to a string does not append to the string [-Wstring-plus-int]
                throw(out_of_range("returning empty node due to the invalid vertexID:"+u));
                                   ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜^˜
GatingHierarchy.cpp:961:73: note: use array indexing to silence this warning
                throw(out_of_range("returning empty node due to the invalid vertexID:"+u));
                                                                                      ^
                                   &                                                  [ ]
In file included from GatingHierarchy.cpp:8:
./include/GatingHierarchy.hpp:64:9: warning: logical not is only applied to the left hand side of this comparison [-Wlogical-not-parentheses]
        if(!u==0)
           ^ ˜˜
bst/boost/graph/graphviz.hpp:270:7: note: in instantiation of function template specialization 'OurVertexPropertyWriterR::operator()<unsigned long>' requested here
      vpw(out, *i); //print vertex attributes
      ^
bst/boost/graph/graphviz.hpp:290:5: note: in instantiation of function template specialization 'boost::write_graphviz<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, nodeProperties, boost::no_property, boost::no_property, boost::listS>, OurVertexPropertyWriterR, boost::default_writer, boost::default_writer, boost::vec_adj_list_vertex_id_map<nodeProperties, unsigned long> >' requested here
  { write_graphviz(out, g, vpw, epw, gpw, get(vertex_index, g)); }
    ^
bst/boost/graph/graphviz.hpp:312:5: note: in instantiation of function template specialization 'boost::write_graphviz<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, nodeProperties, boost::no_property, boost::no_property, boost::listS>, OurVertexPropertyWriterR, boost::default_writer, boost::default_writer>' requested here
    write_graphviz(out, g, vw, dw, gw);
    ^
GatingHierarchy.cpp:627:9: note: in instantiation of function template specialization 'boost::write_graphviz<boost::adjacency_list<boost::vecS, boost::vecS, boost::bidirectionalS, nodeProperties, boost::no_property, boost::no_property, boost::listS>, OurVertexPropertyWriterR>' requested here
        boost::write_graphviz(outputFile,tree,OurVertexPropertyWriterR(tree));
               ^
./include/GatingHierarchy.hpp:64:9: note: add parentheses after the '!' to evaluate the comparison first
        if(!u==0)
           ^
            (   )
./include/GatingHierarchy.hpp:64:9: note: add parentheses around left hand side expression to silence this warning
        if(!u==0)
           ^
           ( )
5 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c GatingSet.cpp -o GatingSet.o
GatingSet.cpp:167:5: warning: delete called on 'transformation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
                                delete curTran;
                                ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:14:
In file included from ./include/flowData.hpp:21:
In file included from bst/boost/archive/text_iarchive.hpp:24:
In file included from bst/boost/archive/basic_text_iarchive.hpp:31:
In file included from bst/boost/archive/detail/common_iarchive.hpp:23:
In file included from bst/boost/archive/detail/interface_iarchive.hpp:22:
In file included from bst/boost/archive/detail/iserializer.hpp:47:
In file included from bst/boost/serialization/extended_type_info_typeid.hpp:37:
bst/boost/serialization/access.hpp:125:9: warning: delete called on 'biexpTrans' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete const_cast<T *>(t);
        ^
bst/boost/serialization/extended_type_info_typeid.hpp:133:39: note: in instantiation of function template specialization 'boost::serialization::access::destroy<biexpTrans>' requested here
        boost::serialization::access::destroy(
                                      ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::serialization::extended_type_info_typeid<biexpTrans>::destroy' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<biexpTrans> >::get_instance' requested here
        return get_instance();
               ^
bst/boost/archive/detail/oserializer.hpp:210:12: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<biexpTrans> >::get_const_instance' requested here
        >::get_const_instance()
           ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::archive::detail::pointer_oserializer<boost::archive::binary_oarchive, biexpTrans>::pointer_oserializer' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: (skipping 31 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return get_instance();
               ^
bst/boost/archive/detail/common_oarchive.hpp:69:18: note: in instantiation of function template specialization 'boost::archive::save<boost::archive::binary_oarchive, const boost::serialization::nvp<const GatingSet> >' requested here
        archive::save(* this->This(), t);
                 ^
bst/boost/archive/basic_binary_oarchive.hpp:75:37: note: in instantiation of function template specialization 'boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
      this->detail_common_oarchive::save_override(t, static_cast<int>(version));
                                    ^
bst/boost/archive/binary_oarchive_impl.hpp:51:47: note: in instantiation of function template specialization 'boost::archive::basic_binary_oarchive<boost::archive::binary_oarchive>::save_override<boost::serialization::nvp<const GatingSet> >' requested here
        this->basic_binary_oarchive<Archive>::save_override(t, 0L);
                                              ^
bst/boost/archive/detail/interface_oarchive.hpp:63:23: note: in instantiation of function template specialization 'boost::archive::binary_oarchive_impl<boost::archive::binary_oarchive, char, std::__1::char_traits<char> >::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
        this->This()->save_override(t, 0);
                      ^
GatingSet.cpp:32:11: note: in instantiation of function template specialization 'boost::archive::detail::interface_oarchive<boost::archive::binary_oarchive>::operator<<<const boost::serialization::nvp<const GatingSet> >' requested here
                        oa << BOOST_SERIALIZATION_NVP(gs);
                           ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:14:
In file included from ./include/flowData.hpp:21:
In file included from bst/boost/archive/text_iarchive.hpp:24:
In file included from bst/boost/archive/basic_text_iarchive.hpp:31:
In file included from bst/boost/archive/detail/common_iarchive.hpp:23:
In file included from bst/boost/archive/detail/interface_iarchive.hpp:22:
In file included from bst/boost/archive/detail/iserializer.hpp:47:
In file included from bst/boost/serialization/extended_type_info_typeid.hpp:37:
bst/boost/serialization/access.hpp:125:9: warning: delete called on 'transformation' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete const_cast<T *>(t);
        ^
bst/boost/serialization/extended_type_info_typeid.hpp:133:39: note: in instantiation of function template specialization 'boost::serialization::access::destroy<transformation>' requested here
        boost::serialization::access::destroy(
                                      ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::serialization::extended_type_info_typeid<transformation>::destroy' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<transformation> >::get_instance' requested here
        return get_instance();
               ^
bst/boost/serialization/void_cast.hpp:183:49: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<transformation> >::get_const_instance' requested here
        & type_info_implementation<Base>::type::get_const_instance(),
                                                ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::serialization::void_cast_detail::void_caster_primitive<biexpTrans, transformation>::void_caster_primitive' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: (skipping 45 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return get_instance();
               ^
bst/boost/archive/detail/common_oarchive.hpp:69:18: note: in instantiation of function template specialization 'boost::archive::save<boost::archive::binary_oarchive, const boost::serialization::nvp<const GatingSet> >' requested here
        archive::save(* this->This(), t);
                 ^
bst/boost/archive/basic_binary_oarchive.hpp:75:37: note: in instantiation of function template specialization 'boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
      this->detail_common_oarchive::save_override(t, static_cast<int>(version));
                                    ^
bst/boost/archive/binary_oarchive_impl.hpp:51:47: note: in instantiation of function template specialization 'boost::archive::basic_binary_oarchive<boost::archive::binary_oarchive>::save_override<boost::serialization::nvp<const GatingSet> >' requested here
        this->basic_binary_oarchive<Archive>::save_override(t, 0L);
                                              ^
bst/boost/archive/detail/interface_oarchive.hpp:63:23: note: in instantiation of function template specialization 'boost::archive::binary_oarchive_impl<boost::archive::binary_oarchive, char, std::__1::char_traits<char> >::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
        this->This()->save_override(t, 0);
                      ^
GatingSet.cpp:32:11: note: in instantiation of function template specialization 'boost::archive::detail::interface_oarchive<boost::archive::binary_oarchive>::operator<<<const boost::serialization::nvp<const GatingSet> >' requested here
                        oa << BOOST_SERIALIZATION_NVP(gs);
                           ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:14:
In file included from ./include/flowData.hpp:21:
In file included from bst/boost/archive/text_iarchive.hpp:24:
In file included from bst/boost/archive/basic_text_iarchive.hpp:31:
In file included from bst/boost/archive/detail/common_iarchive.hpp:23:
In file included from bst/boost/archive/detail/interface_iarchive.hpp:22:
In file included from bst/boost/archive/detail/iserializer.hpp:47:
In file included from bst/boost/serialization/extended_type_info_typeid.hpp:37:
bst/boost/serialization/access.hpp:125:9: warning: delete called on 'flinTrans' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete const_cast<T *>(t);
        ^
bst/boost/serialization/extended_type_info_typeid.hpp:133:39: note: in instantiation of function template specialization 'boost::serialization::access::destroy<flinTrans>' requested here
        boost::serialization::access::destroy(
                                      ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::serialization::extended_type_info_typeid<flinTrans>::destroy' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<flinTrans> >::get_instance' requested here
        return get_instance();
               ^
bst/boost/archive/detail/oserializer.hpp:210:12: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<flinTrans> >::get_const_instance' requested here
        >::get_const_instance()
           ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::archive::detail::pointer_oserializer<boost::archive::binary_oarchive, flinTrans>::pointer_oserializer' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: (skipping 31 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return get_instance();
               ^
bst/boost/archive/detail/common_oarchive.hpp:69:18: note: in instantiation of function template specialization 'boost::archive::save<boost::archive::binary_oarchive, const boost::serialization::nvp<const GatingSet> >' requested here
        archive::save(* this->This(), t);
                 ^
bst/boost/archive/basic_binary_oarchive.hpp:75:37: note: in instantiation of function template specialization 'boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
      this->detail_common_oarchive::save_override(t, static_cast<int>(version));
                                    ^
bst/boost/archive/binary_oarchive_impl.hpp:51:47: note: in instantiation of function template specialization 'boost::archive::basic_binary_oarchive<boost::archive::binary_oarchive>::save_override<boost::serialization::nvp<const GatingSet> >' requested here
        this->basic_binary_oarchive<Archive>::save_override(t, 0L);
                                              ^
bst/boost/archive/detail/interface_oarchive.hpp:63:23: note: in instantiation of function template specialization 'boost::archive::binary_oarchive_impl<boost::archive::binary_oarchive, char, std::__1::char_traits<char> >::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
        this->This()->save_override(t, 0);
                      ^
GatingSet.cpp:32:11: note: in instantiation of function template specialization 'boost::archive::detail::interface_oarchive<boost::archive::binary_oarchive>::operator<<<const boost::serialization::nvp<const GatingSet> >' requested here
                        oa << BOOST_SERIALIZATION_NVP(gs);
                           ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:14:
In file included from ./include/flowData.hpp:21:
In file included from bst/boost/archive/text_iarchive.hpp:24:
In file included from bst/boost/archive/basic_text_iarchive.hpp:31:
In file included from bst/boost/archive/detail/common_iarchive.hpp:23:
In file included from bst/boost/archive/detail/interface_iarchive.hpp:22:
In file included from bst/boost/archive/detail/iserializer.hpp:47:
In file included from bst/boost/serialization/extended_type_info_typeid.hpp:37:
bst/boost/serialization/access.hpp:125:9: warning: delete called on 'logTrans' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete const_cast<T *>(t);
        ^
bst/boost/serialization/extended_type_info_typeid.hpp:133:39: note: in instantiation of function template specialization 'boost::serialization::access::destroy<logTrans>' requested here
        boost::serialization::access::destroy(
                                      ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::serialization::extended_type_info_typeid<logTrans>::destroy' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<logTrans> >::get_instance' requested here
        return get_instance();
               ^
bst/boost/archive/detail/oserializer.hpp:210:12: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<logTrans> >::get_const_instance' requested here
        >::get_const_instance()
           ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::archive::detail::pointer_oserializer<boost::archive::binary_oarchive, logTrans>::pointer_oserializer' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: (skipping 31 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return get_instance();
               ^
bst/boost/archive/detail/common_oarchive.hpp:69:18: note: in instantiation of function template specialization 'boost::archive::save<boost::archive::binary_oarchive, const boost::serialization::nvp<const GatingSet> >' requested here
        archive::save(* this->This(), t);
                 ^
bst/boost/archive/basic_binary_oarchive.hpp:75:37: note: in instantiation of function template specialization 'boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
      this->detail_common_oarchive::save_override(t, static_cast<int>(version));
                                    ^
bst/boost/archive/binary_oarchive_impl.hpp:51:47: note: in instantiation of function template specialization 'boost::archive::basic_binary_oarchive<boost::archive::binary_oarchive>::save_override<boost::serialization::nvp<const GatingSet> >' requested here
        this->basic_binary_oarchive<Archive>::save_override(t, 0L);
                                              ^
bst/boost/archive/detail/interface_oarchive.hpp:63:23: note: in instantiation of function template specialization 'boost::archive::binary_oarchive_impl<boost::archive::binary_oarchive, char, std::__1::char_traits<char> >::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
        this->This()->save_override(t, 0);
                      ^
GatingSet.cpp:32:11: note: in instantiation of function template specialization 'boost::archive::detail::interface_oarchive<boost::archive::binary_oarchive>::operator<<<const boost::serialization::nvp<const GatingSet> >' requested here
                        oa << BOOST_SERIALIZATION_NVP(gs);
                           ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:14:
In file included from ./include/flowData.hpp:21:
In file included from bst/boost/archive/text_iarchive.hpp:24:
In file included from bst/boost/archive/basic_text_iarchive.hpp:31:
In file included from bst/boost/archive/detail/common_iarchive.hpp:23:
In file included from bst/boost/archive/detail/interface_iarchive.hpp:22:
In file included from bst/boost/archive/detail/iserializer.hpp:47:
In file included from bst/boost/serialization/extended_type_info_typeid.hpp:37:
bst/boost/serialization/access.hpp:125:9: warning: delete called on 'linTrans' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete const_cast<T *>(t);
        ^
bst/boost/serialization/extended_type_info_typeid.hpp:133:39: note: in instantiation of function template specialization 'boost::serialization::access::destroy<linTrans>' requested here
        boost::serialization::access::destroy(
                                      ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::serialization::extended_type_info_typeid<linTrans>::destroy' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<linTrans> >::get_instance' requested here
        return get_instance();
               ^
bst/boost/archive/detail/oserializer.hpp:210:12: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<linTrans> >::get_const_instance' requested here
        >::get_const_instance()
           ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::archive::detail::pointer_oserializer<boost::archive::binary_oarchive, linTrans>::pointer_oserializer' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: (skipping 31 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return get_instance();
               ^
bst/boost/archive/detail/common_oarchive.hpp:69:18: note: in instantiation of function template specialization 'boost::archive::save<boost::archive::binary_oarchive, const boost::serialization::nvp<const GatingSet> >' requested here
        archive::save(* this->This(), t);
                 ^
bst/boost/archive/basic_binary_oarchive.hpp:75:37: note: in instantiation of function template specialization 'boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
      this->detail_common_oarchive::save_override(t, static_cast<int>(version));
                                    ^
bst/boost/archive/binary_oarchive_impl.hpp:51:47: note: in instantiation of function template specialization 'boost::archive::basic_binary_oarchive<boost::archive::binary_oarchive>::save_override<boost::serialization::nvp<const GatingSet> >' requested here
        this->basic_binary_oarchive<Archive>::save_override(t, 0L);
                                              ^
bst/boost/archive/detail/interface_oarchive.hpp:63:23: note: in instantiation of function template specialization 'boost::archive::binary_oarchive_impl<boost::archive::binary_oarchive, char, std::__1::char_traits<char> >::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
        this->This()->save_override(t, 0);
                      ^
GatingSet.cpp:32:11: note: in instantiation of function template specialization 'boost::archive::detail::interface_oarchive<boost::archive::binary_oarchive>::operator<<<const boost::serialization::nvp<const GatingSet> >' requested here
                        oa << BOOST_SERIALIZATION_NVP(gs);
                           ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:14:
In file included from ./include/flowData.hpp:21:
In file included from bst/boost/archive/text_iarchive.hpp:24:
In file included from bst/boost/archive/basic_text_iarchive.hpp:31:
In file included from bst/boost/archive/detail/common_iarchive.hpp:23:
In file included from bst/boost/archive/detail/interface_iarchive.hpp:22:
In file included from bst/boost/archive/detail/iserializer.hpp:47:
In file included from bst/boost/serialization/extended_type_info_typeid.hpp:37:
bst/boost/serialization/access.hpp:125:9: warning: delete called on 'scaleTrans' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete const_cast<T *>(t);
        ^
bst/boost/serialization/extended_type_info_typeid.hpp:133:39: note: in instantiation of function template specialization 'boost::serialization::access::destroy<scaleTrans>' requested here
        boost::serialization::access::destroy(
                                      ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::serialization::extended_type_info_typeid<scaleTrans>::destroy' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<scaleTrans> >::get_instance' requested here
        return get_instance();
               ^
bst/boost/archive/detail/oserializer.hpp:210:12: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<scaleTrans> >::get_const_instance' requested here
        >::get_const_instance()
           ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::archive::detail::pointer_oserializer<boost::archive::binary_oarchive, scaleTrans>::pointer_oserializer' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: (skipping 31 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return get_instance();
               ^
bst/boost/archive/detail/common_oarchive.hpp:69:18: note: in instantiation of function template specialization 'boost::archive::save<boost::archive::binary_oarchive, const boost::serialization::nvp<const GatingSet> >' requested here
        archive::save(* this->This(), t);
                 ^
bst/boost/archive/basic_binary_oarchive.hpp:75:37: note: in instantiation of function template specialization 'boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
      this->detail_common_oarchive::save_override(t, static_cast<int>(version));
                                    ^
bst/boost/archive/binary_oarchive_impl.hpp:51:47: note: in instantiation of function template specialization 'boost::archive::basic_binary_oarchive<boost::archive::binary_oarchive>::save_override<boost::serialization::nvp<const GatingSet> >' requested here
        this->basic_binary_oarchive<Archive>::save_override(t, 0L);
                                              ^
bst/boost/archive/detail/interface_oarchive.hpp:63:23: note: in instantiation of function template specialization 'boost::archive::binary_oarchive_impl<boost::archive::binary_oarchive, char, std::__1::char_traits<char> >::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
        this->This()->save_override(t, 0);
                      ^
GatingSet.cpp:32:11: note: in instantiation of function template specialization 'boost::archive::detail::interface_oarchive<boost::archive::binary_oarchive>::operator<<<const boost::serialization::nvp<const GatingSet> >' requested here
                        oa << BOOST_SERIALIZATION_NVP(gs);
                           ^
In file included from GatingSet.cpp:9:
In file included from ./include/GatingSet.hpp:12:
In file included from ./include/GatingHierarchy.hpp:13:
In file included from ./include/populationTree.hpp:11:
In file included from ./include/nodeProperties.hpp:11:
In file included from ./include/POPINDICES.hpp:15:
In file included from ./include/gate.hpp:14:
In file included from ./include/flowData.hpp:21:
In file included from bst/boost/archive/text_iarchive.hpp:24:
In file included from bst/boost/archive/basic_text_iarchive.hpp:31:
In file included from bst/boost/archive/detail/common_iarchive.hpp:23:
In file included from bst/boost/archive/detail/interface_iarchive.hpp:22:
In file included from bst/boost/archive/detail/iserializer.hpp:47:
In file included from bst/boost/serialization/extended_type_info_typeid.hpp:37:
bst/boost/serialization/access.hpp:125:9: warning: delete called on 'fasinhTrans' that has virtual functions but non-virtual destructor [-Wdelete-non-virtual-dtor]
        delete const_cast<T *>(t);
        ^
bst/boost/serialization/extended_type_info_typeid.hpp:133:39: note: in instantiation of function template specialization 'boost::serialization::access::destroy<fasinhTrans>' requested here
        boost::serialization::access::destroy(
                                      ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::serialization::extended_type_info_typeid<fasinhTrans>::destroy' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<fasinhTrans> >::get_instance' requested here
        return get_instance();
               ^
bst/boost/archive/detail/oserializer.hpp:210:12: note: in instantiation of member function 'boost::serialization::singleton<boost::serialization::extended_type_info_typeid<fasinhTrans> >::get_const_instance' requested here
        >::get_const_instance()
           ^
bst/boost/serialization/singleton.hpp:106:7: note: in instantiation of member function 'boost::archive::detail::pointer_oserializer<boost::archive::binary_oarchive, fasinhTrans>::pointer_oserializer' requested here
class singleton_wrapper : public T
      ^
bst/boost/serialization/singleton.hpp:141:16: note: (skipping 129 contexts in backtrace; use -ftemplate-backtrace-limit=0 to see all)
        return get_instance();
               ^
bst/boost/archive/detail/common_oarchive.hpp:69:18: note: in instantiation of function template specialization 'boost::archive::save<boost::archive::binary_oarchive, const boost::serialization::nvp<const GatingSet> >' requested here
        archive::save(* this->This(), t);
                 ^
bst/boost/archive/basic_binary_oarchive.hpp:75:37: note: in instantiation of function template specialization 'boost::archive::detail::common_oarchive<boost::archive::binary_oarchive>::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
      this->detail_common_oarchive::save_override(t, static_cast<int>(version));
                                    ^
bst/boost/archive/binary_oarchive_impl.hpp:51:47: note: in instantiation of function template specialization 'boost::archive::basic_binary_oarchive<boost::archive::binary_oarchive>::save_override<boost::serialization::nvp<const GatingSet> >' requested here
        this->basic_binary_oarchive<Archive>::save_override(t, 0L);
                                              ^
bst/boost/archive/detail/interface_oarchive.hpp:63:23: note: in instantiation of function template specialization 'boost::archive::binary_oarchive_impl<boost::archive::binary_oarchive, char, std::__1::char_traits<char> >::save_override<const boost::serialization::nvp<const GatingSet> >' requested here
        this->This()->save_override(t, 0);
                      ^
GatingSet.cpp:32:11: note: in instantiation of function template specialization 'boost::archive::detail::interface_oarchive<boost::archive::binary_oarchive>::operator<<<const boost::serialization::nvp<const GatingSet> >' requested here
                        oa << BOOST_SERIALIZATION_NVP(gs);
                           ^
8 warnings generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c POPINDICES.cpp -o POPINDICES.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_GatingHierarchy.cpp -o R_GatingHierarchy.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c R_GatingSet.cpp -o R_GatingSet.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c calibrationTable.cpp -o calibrationTable.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c flowData.cpp -o flowData.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c flowJoWorkspace.cpp -o flowJoWorkspace.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c gate.cpp -o gate.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c global.cpp -o global.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c macFlowJoWorkspace.cpp -o macFlowJoWorkspace.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c nodeProperties.cpp -o nodeProperties.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c spline.cpp -o spline.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c transformation.cpp -o transformation.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c winFlowJoWorkspace.cpp -o winFlowJoWorkspace.o
winFlowJoWorkspace.cpp:479:27: warning: '/*' within block comment [-Wcomment]
 * "*[local-name()='edge']/*[local-name()='vertex']" is for ellipsoidGate
                          ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c workspace.cpp -o workspace.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c wsNode.cpp -o wsNode.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/archive_exception.cpp -o bst/libs/serialization/src/archive_exception.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_archive.cpp -o bst/libs/serialization/src/basic_archive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_iarchive.cpp -o bst/libs/serialization/src/basic_iarchive.o
bst/libs/serialization/src/basic_iarchive.cpp:437:23: warning: unused variable 'new_cid' [-Wunused-variable]
        class_id_type new_cid = register_type(bpis_ptr->get_basic_serializer());
                      ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_iserializer.cpp -o bst/libs/serialization/src/basic_iserializer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_oarchive.cpp -o bst/libs/serialization/src/basic_oarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_oserializer.cpp -o bst/libs/serialization/src/basic_oserializer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_pointer_iserializer.cpp -o bst/libs/serialization/src/basic_pointer_iserializer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_pointer_oserializer.cpp -o bst/libs/serialization/src/basic_pointer_oserializer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_serializer_map.cpp -o bst/libs/serialization/src/basic_serializer_map.o
bst/libs/serialization/src/basic_serializer_map.cpp:46:47: warning: unused variable 'result' [-Wunused-variable]
    const std::pair<map_type::iterator, bool> result =
                                              ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_text_iprimitive.cpp -o bst/libs/serialization/src/basic_text_iprimitive.o
In file included from bst/libs/serialization/src/basic_text_iprimitive.cpp:19:
bst/boost/archive/impl/basic_text_iprimitive.ipp:47:10: warning: unused function 'is_whitespace' [-Wunused-function]
    bool is_whitespace(wchar_t t){
         ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_text_oprimitive.cpp -o bst/libs/serialization/src/basic_text_oprimitive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_text_wiprimitive.cpp -o bst/libs/serialization/src/basic_text_wiprimitive.o
In file included from bst/libs/serialization/src/basic_text_wiprimitive.cpp:25:
bst/boost/archive/impl/basic_text_iprimitive.ipp:41:10: warning: unused function 'is_whitespace' [-Wunused-function]
    bool is_whitespace(char t){
         ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_text_woprimitive.cpp -o bst/libs/serialization/src/basic_text_woprimitive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/basic_xml_archive.cpp -o bst/libs/serialization/src/basic_xml_archive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/binary_iarchive.cpp -o bst/libs/serialization/src/binary_iarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/binary_oarchive.cpp -o bst/libs/serialization/src/binary_oarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/binary_wiarchive.cpp -o bst/libs/serialization/src/binary_wiarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/binary_woarchive.cpp -o bst/libs/serialization/src/binary_woarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/codecvt_null.cpp -o bst/libs/serialization/src/codecvt_null.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/extended_type_info.cpp -o bst/libs/serialization/src/extended_type_info.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/extended_type_info_no_rtti.cpp -o bst/libs/serialization/src/extended_type_info_no_rtti.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/extended_type_info_typeid.cpp -o bst/libs/serialization/src/extended_type_info_typeid.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/polymorphic_iarchive.cpp -o bst/libs/serialization/src/polymorphic_iarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/polymorphic_oarchive.cpp -o bst/libs/serialization/src/polymorphic_oarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/shared_ptr_helper.cpp -o bst/libs/serialization/src/shared_ptr_helper.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/stl_port.cpp -o bst/libs/serialization/src/stl_port.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/text_iarchive.cpp -o bst/libs/serialization/src/text_iarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/text_oarchive.cpp -o bst/libs/serialization/src/text_oarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/text_wiarchive.cpp -o bst/libs/serialization/src/text_wiarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/text_woarchive.cpp -o bst/libs/serialization/src/text_woarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/utf8_codecvt_facet.cpp -o bst/libs/serialization/src/utf8_codecvt_facet.o
In file included from bst/libs/serialization/src/utf8_codecvt_facet.cpp:15:
In file included from bst/boost/detail/utf8_codecvt_facet.ipp:13:
bst/boost/detail/utf8_codecvt_facet.hpp:171:17: warning: 'boost::archive::detail::utf8_codecvt_facet::do_length' hides overloaded virtual function [-Woverloaded-virtual]
    virtual int do_length(
                ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:952:17: note: hidden overloaded virtual function 'std::__1::codecvt<wchar_t, char, __mbstate_t>::do_length' declared here: type mismatch at 1st parameter ('state_type &' (aka '__mbstate_t &') vs 'const std::mbstate_t &' (aka 'const __mbstate_t &'))
    virtual int do_length(state_type&, const extern_type* __frm, const extern_type* __end, size_t __mx) const;
                ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/void_cast.cpp -o bst/libs/serialization/src/void_cast.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/xml_archive_exception.cpp -o bst/libs/serialization/src/xml_archive_exception.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/xml_grammar.cpp -o bst/libs/serialization/src/xml_grammar.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/xml_iarchive.cpp -o bst/libs/serialization/src/xml_iarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/xml_oarchive.cpp -o bst/libs/serialization/src/xml_oarchive.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/xml_wgrammar.cpp -o bst/libs/serialization/src/xml_wgrammar.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/xml_wiarchive.cpp -o bst/libs/serialization/src/xml_wiarchive.o
In file included from bst/libs/serialization/src/xml_wiarchive.cpp:37:
In file included from bst/boost/archive/impl/xml_wiarchive_impl.ipp:38:
In file included from bst/boost/archive/detail/utf8_codecvt_facet.hpp:15:
bst/boost/detail/utf8_codecvt_facet.hpp:171:17: warning: 'boost::archive::detail::utf8_codecvt_facet::do_length' hides overloaded virtual function [-Woverloaded-virtual]
    virtual int do_length(
                ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:952:17: note: hidden overloaded virtual function 'std::__1::codecvt<wchar_t, char, __mbstate_t>::do_length' declared here: type mismatch at 1st parameter ('state_type &' (aka '__mbstate_t &') vs 'const std::mbstate_t &' (aka 'const __mbstate_t &'))
    virtual int do_length(state_type&, const extern_type* __frm, const extern_type* __end, size_t __mx) const;
                ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/serialization/src/xml_woarchive.cpp -o bst/libs/serialization/src/xml_woarchive.o
In file included from bst/libs/serialization/src/xml_woarchive.cpp:23:
In file included from bst/boost/archive/impl/xml_woarchive_impl.ipp:42:
In file included from bst/boost/archive/detail/utf8_codecvt_facet.hpp:15:
bst/boost/detail/utf8_codecvt_facet.hpp:171:17: warning: 'boost::archive::detail::utf8_codecvt_facet::do_length' hides overloaded virtual function [-Woverloaded-virtual]
    virtual int do_length(
                ^
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/__locale:952:17: note: hidden overloaded virtual function 'std::__1::codecvt<wchar_t, char, __mbstate_t>::do_length' declared here: type mismatch at 1st parameter ('state_type &' (aka '__mbstate_t &') vs 'const std::mbstate_t &' (aka 'const __mbstate_t &'))
    virtual int do_length(state_type&, const extern_type* __frm, const extern_type* __end, size_t __mx) const;
                ^
1 warning generated.
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/c_regex_traits.cpp -o bst/libs/regex/src/c_regex_traits.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/cpp_regex_traits.cpp -o bst/libs/regex/src/cpp_regex_traits.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/cregex.cpp -o bst/libs/regex/src/cregex.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/fileiter.cpp -o bst/libs/regex/src/fileiter.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/icu.cpp -o bst/libs/regex/src/icu.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/instances.cpp -o bst/libs/regex/src/instances.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/posix_api.cpp -o bst/libs/regex/src/posix_api.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/regex.cpp -o bst/libs/regex/src/regex.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/regex_debug.cpp -o bst/libs/regex/src/regex_debug.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/regex_raw_buffer.cpp -o bst/libs/regex/src/regex_raw_buffer.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/regex_traits_defaults.cpp -o bst/libs/regex/src/regex_traits_defaults.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/static_mutex.cpp -o bst/libs/regex/src/static_mutex.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/usinstances.cpp -o bst/libs/regex/src/usinstances.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/w32_regex_traits.cpp -o bst/libs/regex/src/w32_regex_traits.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/wc_regex_traits.cpp -o bst/libs/regex/src/wc_regex_traits.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/wide_posix_api.cpp -o bst/libs/regex/src/wide_posix_api.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DROUT -Wno-deprecated -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/libxml2 -ftemplate-depth=900 -Ibst/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c bst/libs/regex/src/winstances.cpp -o bst/libs/regex/src/winstances.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o flowWorkspace.so GatingHierarchy.o GatingSet.o POPINDICES.o R_GatingHierarchy.o R_GatingSet.o calibrationTable.o flowData.o flowJoWorkspace.o gate.o global.o macFlowJoWorkspace.o nodeProperties.o spline.o transformation.o winFlowJoWorkspace.o workspace.o wsNode.o bst/libs/serialization/src/archive_exception.o bst/libs/serialization/src/basic_archive.o bst/libs/serialization/src/basic_iarchive.o bst/libs/serialization/src/basic_iserializer.o bst/libs/serialization/src/basic_oarchive.o bst/libs/serialization/src/basic_oserializer.o bst/libs/serialization/src/basic_pointer_iserializer.o bst/libs/serialization/src/basic_pointer_oserializer.o bst/libs/serialization/src/basic_serializer_map.o bst/libs/serialization/src/basic_text_iprimitive.o bst/libs/serialization/src/basic_text_oprimitive.o bst/libs/serialization/src/basic_text_wiprimitive.o bst/libs/serialization/src/basic_text_woprimitive.o bst/libs/serialization/src/basic_xml_archive.o bst/libs/serialization/src/binary_iarchive.o bst/libs/serialization/src/binary_oarchive.o bst/libs/serialization/src/binary_wiarchive.o bst/libs/serialization/src/binary_woarchive.o bst/libs/serialization/src/codecvt_null.o bst/libs/serialization/src/extended_type_info.o bst/libs/serialization/src/extended_type_info_no_rtti.o bst/libs/serialization/src/extended_type_info_typeid.o bst/libs/serialization/src/polymorphic_iarchive.o bst/libs/serialization/src/polymorphic_oarchive.o bst/libs/serialization/src/shared_ptr_helper.o bst/libs/serialization/src/stl_port.o bst/libs/serialization/src/text_iarchive.o bst/libs/serialization/src/text_oarchive.o bst/libs/serialization/src/text_wiarchive.o bst/libs/serialization/src/text_woarchive.o bst/libs/serialization/src/utf8_codecvt_facet.o bst/libs/serialization/src/void_cast.o bst/libs/serialization/src/xml_archive_exception.o bst/libs/serialization/src/xml_grammar.o bst/libs/serialization/src/xml_iarchive.o bst/libs/serialization/src/xml_oarchive.o bst/libs/serialization/src/xml_wgrammar.o bst/libs/serialization/src/xml_wiarchive.o bst/libs/serialization/src/xml_woarchive.o bst/libs/regex/src/c_regex_traits.o bst/libs/regex/src/cpp_regex_traits.o bst/libs/regex/src/cregex.o bst/libs/regex/src/fileiter.o bst/libs/regex/src/icu.o bst/libs/regex/src/instances.o bst/libs/regex/src/posix_api.o bst/libs/regex/src/regex.o bst/libs/regex/src/regex_debug.o bst/libs/regex/src/regex_raw_buffer.o bst/libs/regex/src/regex_traits_defaults.o bst/libs/regex/src/static_mutex.o bst/libs/regex/src/usinstances.o bst/libs/regex/src/w32_regex_traits.o bst/libs/regex/src/wc_regex_traits.o bst/libs/regex/src/wide_posix_api.o bst/libs/regex/src/winstances.o -lxml2 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
cp flowWorkspace.so libflowWorkspace.dylib 
cp libflowWorkspace.dylib ../inst/lib
rm libflowWorkspace.dylib
installing to /Users/biocbuild/bbs-2.14-bioc/meat/flowWorkspace.Rcheck/flowWorkspace/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 (flowWorkspace)

name	user	system	elapsed
GatingHierarchy-class	4.825	0.199	5.106
GatingSet-class	2.461	0.190	2.659
GatingSetList-class	0.003	0.000	0.004
add	0.002	0.000	0.003
clone	0.001	0.000	0.001
flowJoWorkspace-class	0.068	0.006	0.076
flowWorkspace.par.get	0.002	0.000	0.002
getCompensationMatrices	0.000	0.000	0.001
getData-methods	0.001	0.000	0.000
getGate	0.000	0.000	0.001
getIndices	0.001	0.000	0.001
getKeywords	0.298	0.041	0.390
getNodes	0.001	0.000	0.001
getParent	0.001	0.000	0.001
getPopStats	0.001	0.000	0.001
getSample	0.001	0.000	0.001
getSampleGroups	0.001	0.000	0.001
getSamples	0.001	0.000	0.000
getSingleCellExpression	0.001	0.000	0.001
getTransformations	0.000	0.000	0.001
keyword	0.001	0.000	0.001
loglevel	0.001	0.000	0.001
mkformula	0.002	0.000	0.003
openWorkspace	0	0	0
parseWorkspace	0.001	0.000	0.001
plot-methods	0.001	0.000	0.001
plotGate-methods	0.002	0.000	0.002
plotPopCV-methods	0.001	0.000	0.001
sampleNames	0.001	0.000	0.000
save_gs	0.001	0.000	0.001
setNode-methods	0.001	0.000	0.001