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  • Building OLB for MacOS

    I recently built the old GAPipeline v1.5 software for MacOS. I'm now trying to build Illumina's newer OLB 1.6.0 for MacOS [10.6] and I'm looking for anyone who has had success in doing so.

    So far I have installed the following packages:
    * fftw (float enabled) (from source)
    * gnuplot (from macports)
    * imagemagick (from macports)
    * p5-xml-simple [XML::Simple] (from macports)
    * doxygen (from macports)

    In order for boost to build, I had to do the following: [MacOS 10.6 only]
    * Untar opt/boost_1_37_0.tar.gz
    * Edit line 25 of boost_1_37_0/tools/build/v2/tools/darwin.jam to be
    10.6 10.5 10.4 10.3 10.2 10.1
    * Retar and replace opt/boost_1_37_0.tar.gz with the modified version.

    [In case anyone is going to site this as the problem, I get the same errors in 10.5]


    I also edit c++/common/Sequence.hh to have the following line:
    #include <sys/types.h>


    After this, i run make and get the following output when compiling PairFileXmlSerialization.cpp:

    [ 13%] Building CXX object c++/common/CMakeFiles/ga_common.dir/PairFileXmlSerialization.cpp.o
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp: In function ‘void ga::common::savePairXml(const ga::common::PairProperties&, const std::string&)’:
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:33: error: ‘assign’ is not a namespace-name
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:33: error: expected namespace-name before ‘;’ token
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2ManyAlignmentsFound]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/iserializer.hpp:152: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read2ManyAlignmentsFound’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2SingleAlignmentFound]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/iserializer.hpp:152: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read2SingleAlignmentFound’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1SingleAlignmentFound]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/iserializer.hpp:152: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read1SingleAlignmentFound’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2NM]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2NM]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2NM]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/iserializer.hpp:152: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2NM]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read2NM’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1NM]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1NM]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1NM]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/iserializer.hpp:152: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1NM]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read1NM’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2Repeat]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2Repeat]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2Repeat]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/iserializer.hpp:152: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = ga::common::Read2Repeat]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read2Repeat’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1Repeat]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1Repeat]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1Repeat]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/iserializer.hpp:152: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1Repeat]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read1Repeat’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2ManyAlignmentsFound]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/oserializer.hpp:144: instantiated from ‘void boost::archive::detail:serializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read2ManyAlignmentsFound’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2SingleAlignmentFound]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/oserializer.hpp:144: instantiated from ‘void boost::archive::detail:serializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read2SingleAlignmentFound’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1SingleAlignmentFound]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/oserializer.hpp:144: instantiated from ‘void boost::archive::detail:serializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1SingleAlignmentFound]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read1SingleAlignmentFound’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2NM]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2NM]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2NM]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/oserializer.hpp:144: instantiated from ‘void boost::archive::detail:serializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2NM]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read2NM’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1NM]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1NM]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1NM]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/oserializer.hpp:144: instantiated from ‘void boost::archive::detail:serializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1NM]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read1NM’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2Repeat]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2Repeat]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2Repeat]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/oserializer.hpp:144: instantiated from ‘void boost::archive::detail:serializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::xml_oarchive, T = ga::common::Read2Repeat]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read2Repeat’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp: In static member function ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1Repeat]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1Repeat]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1Repeat]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/oserializer.hpp:144: instantiated from ‘void boost::archive::detail:serializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1Repeat]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: error: ‘struct ga::common::Read1Repeat’ has no member named ‘serialize’
    /Users/myuser/OLB-1.6.0/c++/common/PairProperties.hh: At global scope:
    /Users/myuser/OLB-1.6.0/c++/common/PairProperties.hh: In instantiation of ‘void ga::common::Read1ManyAlignmentsFound::serialize(Archive&, unsigned int) [with Archive = boost::archive::xml_iarchive]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: instantiated from ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/iserializer.hpp:152: instantiated from ‘void boost::archive::detail::iserializer<Archive, T>::load_object_data(boost::archive::detail::basic_iarchive&, void*, unsigned int) const [with Archive = boost::archive::xml_iarchive, T = ga::common::Read1ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/c++/common/PairProperties.hh:498: warning: unused parameter ‘ar’
    /Users/myuser/OLB-1.6.0/c++/common/PairProperties.hh: In instantiation of ‘void ga::common::Read1ManyAlignmentsFound::serialize(Archive&, unsigned int) [with Archive = boost::archive::xml_oarchive]’:
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/access.hpp:109: instantiated from ‘static void boost::serialization::access::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:74: instantiated from ‘void boost::serialization::serialize(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/serialization/serialization.hpp:133: instantiated from ‘void boost::serialization::serialize_adl(Archive&, T&, unsigned int) [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/opt/include/boost/archive/detail/oserializer.hpp:144: instantiated from ‘void boost::archive::detail:serializer<Archive, T>::save_object_data(boost::archive::detail::basic_oarchive&, const void*) const [with Archive = boost::archive::xml_oarchive, T = ga::common::Read1ManyAlignmentsFound]’
    /Users/myuser/OLB-1.6.0/c++/common/PairFileXmlSerialization.cpp:65: instantiated from here
    /Users/myuser/OLB-1.6.0/c++/common/PairProperties.hh:498: warning: unused parameter ‘ar’
    make[3]: *** [c++/common/CMakeFiles/ga_common.dir/PairFileXmlSerialization.cpp.o] Error 1
    make[2]: *** [c++/common/CMakeFiles/ga_common.dir/all] Error 2
    make[1]: *** [all] Error 2
    make: *** [all] Error 2
    Does anyone have any knowledge as to what these boost errors are all about? It compiles correctly on both Redhat and Ubuntu, but can't quite do it on MacOS.

    Thank you. Any help or pointers will be much appreciated,

    Carl

  • #2
    Hello Carl,
    I've read your post just after Illumina released OLB 1.8.0... I've tried to install the latest version and I've succeeded with the following procedure:

    Things I already had on my system
    • ImageMagick (Macports)


    Things I had to install
    • fftw-3-single (Macports)
    • gnuplot (v 4.4, Macports)
    • boost ( v 1.43, Macports)
    • XML::Simple (CPAN)


    I've skipped doxygen right now...

    I've patched three files:

    Code:
    $ diff -u validate.sh validate.sh.1
    --- validate.sh	2010-08-03 10:27:56.000000000 +0200
    +++ validate.sh.1	2010-08-03 11:46:57.000000000 +0200
    @@ -346,7 +346,7 @@
     
         log_msg "Wrote source to ${tmp_src_fn}."
     
    -    cmd="g++ -o ${tmp_bin_fn} ${tmp_src_fn} -I/opt/local/include -L/opt/local/lib -l${lib_str}"
    +    cmd="g++ -o ${tmp_bin_fn} ${tmp_src_fn} -l${lib_str}"
     
         cmd_out=`$cmd 2>&1`
         cmd_res=$?
    To make it search fftw3f installed by macports

    Code:
    diff -u c++/CMakeLists.txt c++/CMakeLists.txt.1
    --- c++/CMakeLists.txt	2010-08-03 10:42:17.000000000 +0200
    +++ c++/CMakeLists.txt.1	2010-08-03 11:48:00.000000000 +0200
    @@ -79,12 +79,12 @@
     macro(ga_find_library name header library)
     if    (NOT ${name}_INCLUDE_DIR)
         find_path(${name}_INCLUDE_DIR ${header} 
    -              HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH /opt/local/include)
    +              HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH)
     endif (NOT ${name}_INCLUDE_DIR)
     if    (${name}_INCLUDE_DIR AND NOT ${name}_LIBRARY)
         find_library(${name}_LIBRARY 
                      NAMES "${GA_LIBRARY_PREFIX}${library}${GA_LIBRARY_SUFFIX}"
    -                 HINTS ENV LIBRARY_PATH /opt/local/lib)
    +                 HINTS ENV LIBRARY_PATH)
     endif (${name}_INCLUDE_DIR AND NOT ${name}_LIBRARY)
     if(${name}_INCLUDE_DIR AND ${name}_LIBRARY)
         set (HAVE_${name} ${${name}_LIBRARY})
    To be sure MacPorts path is searched at build time

    Code:
    $ diff -u c++/common/Sequence.hh c++/common/Sequence.hh.1
    --- c++/common/Sequence.hh	2010-08-03 11:31:45.000000000 +0200
    +++ c++/common/Sequence.hh.1	2010-08-03 11:47:23.000000000 +0200
    @@ -22,7 +22,6 @@
     
     #include <string>
     #include <vector>
    -#include <sys/types.h>
     
     #include "Spot.hh"
     #include "FilteringStreams.hh"
    You already did this...

    After that make && make install works fine (with some warnings, of course).

    HTH

    d

    Comment


    • #3
      Hi!

      Another solution is to compile fftw by hand using enable-single option.

      Code:
      ./configure --enable-single
      make
      make install
      And i've replace uint by unsigned int in
      /c++/common/Alignment.hh, Alignment.cpp, Sequence.hh and Sequence.cpp
      /c++/common/cppunit/testSequence.cpp


      Jeremy

      Comment


      • #4
        Originally posted by Mercutio View Post
        Hi!
        Another solution is to compile fftw by hand using enable-single option.
        True but I personally prefer to use MacPorts so that everything is handled by a single application (port).

        d

        Comment


        • #5
          OLB v1.6 still gives me the errors after patching. I'm new on this project so I just registered with Illumina. In a couple days I should be able to download the newest source. I'll let you know if I run into any other issues.

          Comment

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