<div dir="ltr">After updating the bioconductor packages to the Bioc 2.14 release, I ran in to this failure on Mac OS X 10.9 with the clang compilers from Xcode 5.1.1. Interestingly, this failure doesn't occur on Mac OS X 10.8 with the clang compilers from Xcode 5.1.1 which suggests it somehow libc++ related. The error below is suppressed on 10.9 f I append -stdlib=libstdc++ to the compile line so it is definitely libc++ specific. <div>
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<div> Jack</div><div>ps The error I see in mzR using Rcpp 0.11.1 is…</div><div><br></div><div>clang++ -I/sw/Library/Frameworks/R.framework/Versions/3.1/Resources/include -DNDEBUG -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB -D_NODEBUG -I/sw/include -I"/sw/lib/R/3.1/site-library/Rcpp/include" -fPIC -g -O3 -c boost/regex/src/posix_api.cpp -o boost/regex/src/posix_api.o</div>
<div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:149:9: error: too few template arguments for class template 'vector'</div>
<div> std::vector<name> m_sub_names;</div><div> ^</div><div>./boost/detail/container_fwd.hpp:82:47: note: template is declared here</div><div> template <class T, class Allocator> class vector;</div>
<div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div>
<div>./boost/regex/v4/basic_regex.hpp:131:21: error: too few template arguments for class template 'vector'</div><div> typename std::vector<name>::const_iterator pos = std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);</div>
<div> ^</div><div>./boost/detail/container_fwd.hpp:82:47: note: template is declared here</div><div> template <class T, class Allocator> class vector;</div><div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div>
<div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:131:35: error: expected a qualified name after 'typename'</div>
<div> typename std::vector<name>::const_iterator pos = std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);</div><div> ^</div><div>./boost/regex/v4/basic_regex.hpp:131:35: error: unknown type name 'const_iterator'</div>
<div>./boost/regex/v4/basic_regex.hpp:141:21: error: too few template arguments for class template 'vector'</div><div> typename std::vector<name>::const_iterator pos = std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);</div>
<div> ^</div><div>./boost/detail/container_fwd.hpp:82:47: note: template is declared here</div><div> template <class T, class Allocator> class vector;</div><div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div>
<div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:141:35: error: expected a qualified name after 'typename'</div>
<div> typename std::vector<name>::const_iterator pos = std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);</div><div> ^</div><div>./boost/regex/v4/basic_regex.hpp:141:35: error: unknown type name 'const_iterator'</div>
<div>./boost/regex/v4/basic_regex.hpp:163:12: error: too few template arguments for class template 'vector'</div><div> std::vector<Other> v;</div><div> ^</div><div>./boost/detail/container_fwd.hpp:82:47: note: template is declared here</div>
<div> template <class T, class Allocator> class vector;</div><div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div>
<div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:228:9: error: too few template arguments for class template 'vector'</div><div> std::vector<</div><div> ^</div>
<div>./boost/detail/container_fwd.hpp:82:47: note: template is declared here</div><div> template <class T, class Allocator> class vector;</div><div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div>
<div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:269:9: error: too few template arguments for class template 'basic_string'</div>
<div> std::basic_string<charT> BOOST_REGEX_CALL str()const</div><div> ^</div><div>./boost/detail/container_fwd.hpp:63:65: note: template is declared here</div><div> template <class charT, class traits, class Allocator> class basic_string;</div>
<div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div>
<div>./boost/regex/v4/basic_regex.hpp:271:12: error: too few template arguments for class template 'basic_string'</div><div> std::basic_string<charT> result;</div><div> ^</div><div>./boost/detail/container_fwd.hpp:63:65: note: template is declared here</div>
<div> template <class charT, class traits, class Allocator> class basic_string;</div><div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div>
<div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:273:24: error: too few template arguments for class template 'basic_string'</div>
<div> result = std::basic_string<charT>(this->m_expression, this->m_expression_len);</div><div> ^</div><div>./boost/detail/container_fwd.hpp:63:65: note: template is declared here</div>
<div> template <class charT, class traits, class Allocator> class basic_string;</div><div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div>
<div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:285:68: error: implicit instantiation of undefined template 'std::pair<unsigned long, unsigned long>'</div>
<div> std::pair<const_iterator, const_iterator> p(expression() + pi.first, expression() + pi.second);</div><div> ^</div><div>./boost/detail/container_fwd.hpp:92:42: note: template is declared here</div>
<div> template <class T1, class T2> struct pair;</div><div> ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div>
<div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:527:9: error: too few template arguments for class template 'basic_string'</div><div> std::basic_string<charT> BOOST_REGEX_CALL str()const</div>
<div> ^</div><div>./boost/detail/container_fwd.hpp:63:65: note: template is declared here</div><div> template <class charT, class traits, class Allocator> class basic_string;</div><div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div>
<div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:67:</div><div>./boost/regex/v4/basic_regex.hpp:529:52: error: too few template arguments for class template 'basic_string'</div>
<div> return m_pimpl.get() ? m_pimpl->str() : std::basic_string<charT>();</div><div> ^</div><div>./boost/detail/container_fwd.hpp:63:65: note: template is declared here</div>
<div> template <class charT, class traits, class Allocator> class basic_string;</div><div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div>
<div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:70:</div><div>./boost/regex/v4/basic_regex_creator.hpp:140:26: error: too few template arguments for class template 'vector'</div>
<div> typedef typename std::vector<digraph_type>::const_iterator list_iterator;</div><div> ^</div><div>./boost/detail/container_fwd.hpp:82:47: note: template is declared here</div><div> template <class T, class Allocator> class vector;</div>
<div> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^</div><div>In file included from boost/regex/src/posix_api.cpp:22:</div><div>In file included from ./boost/regex.hpp:31:</div><div>In file included from ./boost/regex/v4/regex.hpp:70:</div>
<div>./boost/regex/v4/basic_regex_creator.hpp:140:48: error: expected a qualified name after 'typename'</div><div> typedef typename std::vector<digraph_type>::const_iterator list_iterator;</div><div> ^</div>
<div>./boost/regex/v4/basic_regex_creator.hpp:140:62: error: expected ';' at end of declaration list</div><div> typedef typename std::vector<digraph_type>::const_iterator list_iterator;</div><div> ^</div>
<div> ;</div><div>./boost/regex/v4/basic_regex_creator.hpp:141:4: error: unknown type name 'list_iterator'</div><div> list_iterator singles_begin()const</div>
<div> ^</div><div>fatal error: too many errors emitted, stopping now [-ferror-limit=]</div><div>20 errors generated.</div><div><br></div></div></div></div>