flowWorkspace 3.10.09
Greg Finak ,Mike Jiang
| Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/flowWorkspace | | Last Changed Rev: 91108 / Revision: 95116 | | Last Changed Date: 2014-06-09 15:12:19 -0700 (Mon, 09 Jun 2014) |
| zin2 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK |
| petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | [ OK ] |
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###
### Running command:
###
### rm -rf flowWorkspace.buildbin-libdir && mkdir flowWorkspace.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh flowWorkspace_3.10.09.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R flowWorkspace.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=flowWorkspace.buildbin-libdir flowWorkspace_3.10.09.tar.gz'
>>>>>>>
* 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.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.3.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libquadmath.0.dylib" "flowWorkspace.buildbin-libdir/flowWorkspace/libs//flowWorkspace.so"