title: How do I troubleshoot boost library/header inclusion via autoconf/automake?
body: <p>I'm new to autom4te, and I'm trying to use autoconf/automake to build and link a C++ program on multiple architectures. Complicating the linking is the fact that the project requires boost (filesystem, system, program_options).</p>
  
  <p>I'm using boost.m4 (from <a href="http://github.com/tsuna/boost.m4/tree/" rel="nofollow noreferrer">http://github.com/tsuna/boost.m4/tree/</a>), and it seems to locate all the libraries and headers successfully.</p>
  
  <p>Unfortunately, linking still fails, leaving me confused.</p>
  
  <p>These are the relevant lines of <code>configure.ac</code>:</p>
  
  <pre><code>AC_CONFIG_MACRO_DIR([m4])
  # ...
  AC_PROG_CXX
  AC_PROG_LIBTOOL
  # ...
  BOOST_REQUIRE([1.41.0])
  BOOST_FILESYSTEM
  BOOST_SYSTEM
  BOOST_PROGRAM_OPTIONS
  # ...
  </code></pre>
  
  <p>And in <code>src/Makefile.am</code>:</p>
  
  <pre><code>bin_PROGRAMS = phenomatrix
  phenomatrix_CXXFLAGS = $(BOOST_CPPFLAGS)
  phenomatrix_LDFLAGS = $(BOOST_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) # $(BOOST_SYSTEM_LIB) $(BOOST_PROGRAM_OPTIONS_LIB) $(BOOST_FILESYSTEM_LIB)
  phenomatrix_LIBS = $(BOOST_SYSTEM_LIBS) $(BOOST_FILESYSTEM_LIBS) $(BOOST_PROGRAM_OPTIONS_LIBS)
  phenomatrix_SOURCES = adjacency_list.cpp distance.cpp genephene.cpp knearest.cpp marshall.cpp oracle.cpp type_shield.cpp avgmindist.cpp euclidean.cpp hypergeometric.cpp main.cpp mindist.cpp partialbayes.cpp utilities.cpp
  </code></pre>
  
  <p>These give no errors, and it even manages to find the libraries and headers:</p>
  
  <pre><code>checking for Boost headers version &gt;= 104100... yes
  checking for Boost's header version... 1_41
  checking for the toolset name used by Boost for g++... gcc44 -gcc
  checking boost/system/error_code.hpp usability... yes
  checking boost/system/error_code.hpp presence... yes
  checking for boost/system/error_code.hpp... yes
  checking for the Boost system library... yes
  checking boost/filesystem/path.hpp usability... yes
  checking boost/filesystem/path.hpp presence... yes
  checking for boost/filesystem/path.hpp... yes
  checking for the Boost filesystem library... yes
  checking for boost/system/error_code.hpp... (cached) yes
  checking for the Boost system library... (cached) yes
  checking boost/program_options.hpp usability... yes
  checking boost/program_options.hpp presence... yes
  checking for boost/program_options.hpp... yes
  checking for the Boost program_options library... yes
  </code></pre>
  
  <p>But then, when I run <code>make</code>, I get errors:</p>
  
  <pre><code>libtool: link: g++ -g -O2 -o phenomatrix phenomatrix-adjacency_list.o phenomatrix-distance.o phenomatrix-genephene.o phenomatrix-knearest.o phenomatrix-marshall.o phenomatrix-oracle.o phenomatrix-type_shield.o phenomatrix-avgmindist.o phenomatrix-euclidean.o phenomatrix-hypergeometric.o phenomatrix-main.o phenomatrix-mindist.o phenomatrix-partialbayes.o phenomatrix-utilities.o  -L/usr/local/lib -Wl,-rpath -Wl,/usr/local/lib
  phenomatrix-adjacency_list.o: In function `__static_initialization_and_destruction_0':
  /usr/local/include/boost/system/error_code.hpp:208: undefined reference to `boost::system::get_system_category()'
  /usr/local/include/boost/system/error_code.hpp:209: undefined reference to `boost::system::get_generic_category()'
  /usr/local/include/boost/system/error_code.hpp:214: undefined reference to `boost::system::get_generic_category()'
  /usr/local/include/boost/system/error_code.hpp:215: undefined reference to `boost::system::get_generic_category()'
  /usr/local/include/boost/system/error_code.hpp:216: undefined reference to `boost::system::get_system_category()'
  </code></pre>
  
  <p>which repeat ad nauseum.</p>
  
  <p>I'm not even sure how to go about testing to see if it's including the right directories. Yes, I understand that there's a <code>-t</code> flag on g++, but I don't exactly know how to pass that (from within autom4te).</p>
  
  <p>I gather this has something to do with multiple versions of the boost libs and headers on the same machine, and there's not much I can do about that.</p>