[Rcpp-devel] no matching function for call in mzR on Mac after Rcpp 0.11.0 update
Laurent Gatto
lg390 at cam.ac.uk
Wed May 14 10:07:17 CEST 2014
We hope to be able to provide a fix soon - will get back to you later
today. Apologies for the inconvenience.
Laurent
On 14 May 2014 05:49, Kevin Ushey <kevinushey at gmail.com> wrote:
> Hi Jack,
>
> I've already brought this up with the package maintainer. It's because
> they bundle an old, broken version of boost. I asked them to fix it; I
> guess they haven't (the BioC build reports also show it failing on
> Mavericks) I've appended a copy of my e-mail at the end of this just
> so you know what's up (and maybe others having problems will stumble
> upon it).
>
> A local fix would involve removing the (broken, illegal) forward declarations.
>
> The error you saw before, re reference classes, was something separate
> -- that was indeed our bug, and is fixed in the current version of
> Rcpp on CRAN.
>
> Thanks,
> Kevin
>
> ---
>
> Hi Bernd, Nicolas,
>
> I'm unable to install mzR from source. Here's the script I use:
>
> #!/usr/bin/env sh
>
> cd ~
> mkdir .mzR
> cd .mzR
> wget http://www.bioconductor.org/packages/devel/bioc/src/contrib/mzR_1.9.8.tar.gz
> R CMD INSTALL mzR_1.9.8.tar.gz
>
> This gives me the same error as Nicolas sees:
>
> In file included from pwiz/data/msdata/DefaultReaderList.cpp:40:
>
> In file included from ./boost/regex.hpp:31:
> In file included from ./boost/regex/v4/regex.hpp:67:
> ./boost/regex/v4/basic_regex.hpp:149:9: error: too few template
> arguments for class
> template 'vector'
> std::vector<name> m_sub_names;
> ^
> ./boost/detail/container_fwd.hpp:82:47: note: template is declared here
> template <class T, class Allocator> class vector;
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>
> This is actually a case of boost doing something it shouldn't -- it's
> trying to forward-declare std::vector, but one cannot assume the
> template structure of a vector is of <class T, class Allocator> -- in
> particular this breaks on clang with libc++. See e.g.
> http://stackoverflow.com/questions/307343/forward-declare-an-stl-container
>
> One can work around this by forcing the following Makevars flags:
>
> PKG_CXXFLAGS=-std=gnu++11 -stdlib=libstdc++
>
> However, this will only work if both Rcpp and mzR are built with the
> same flags, and using libstdc++ kind of defeats the purpose of using
> clang...
>
> I'm sure you'll get some mail from Dan Tenenbaum when he tries to
> build the package on the new Mavericks machines, so I think you will
> have to either update the version of boost packaged with mzR, or fix
> the forward declarations that it tries to use.
>
> Cheers,
> Kevin
>
> On Tue, May 13, 2014 at 8:52 PM, Jack Howarth
> <howarth.mailing.lists at gmail.com> wrote:
>> 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.
>> Jack
>> ps The error I see in mzR using Rcpp 0.11.1 is…
>>
>> 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
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:149:9: error: too few template arguments
>> for class template 'vector'
>> std::vector<name> m_sub_names;
>> ^
>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared here
>> template <class T, class Allocator> class vector;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:131:21: error: too few template arguments
>> for class template 'vector'
>> typename std::vector<name>::const_iterator pos =
>> std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);
>> ^
>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared here
>> template <class T, class Allocator> class vector;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:131:35: error: expected a qualified name
>> after 'typename'
>> typename std::vector<name>::const_iterator pos =
>> std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);
>> ^
>> ./boost/regex/v4/basic_regex.hpp:131:35: error: unknown type name
>> 'const_iterator'
>> ./boost/regex/v4/basic_regex.hpp:141:21: error: too few template arguments
>> for class template 'vector'
>> typename std::vector<name>::const_iterator pos =
>> std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);
>> ^
>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared here
>> template <class T, class Allocator> class vector;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:141:35: error: expected a qualified name
>> after 'typename'
>> typename std::vector<name>::const_iterator pos =
>> std::lower_bound(m_sub_names.begin(), m_sub_names.end(), t);
>> ^
>> ./boost/regex/v4/basic_regex.hpp:141:35: error: unknown type name
>> 'const_iterator'
>> ./boost/regex/v4/basic_regex.hpp:163:12: error: too few template arguments
>> for class template 'vector'
>> std::vector<Other> v;
>> ^
>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared here
>> template <class T, class Allocator> class vector;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:228:9: error: too few template arguments
>> for class template 'vector'
>> std::vector<
>> ^
>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared here
>> template <class T, class Allocator> class vector;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:269:9: error: too few template arguments
>> for class template 'basic_string'
>> std::basic_string<charT> BOOST_REGEX_CALL str()const
>> ^
>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared here
>> template <class charT, class traits, class Allocator> class
>> basic_string;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:271:12: error: too few template arguments
>> for class template 'basic_string'
>> std::basic_string<charT> result;
>> ^
>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared here
>> template <class charT, class traits, class Allocator> class
>> basic_string;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:273:24: error: too few template arguments
>> for class template 'basic_string'
>> result = std::basic_string<charT>(this->m_expression,
>> this->m_expression_len);
>> ^
>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared here
>> template <class charT, class traits, class Allocator> class
>> basic_string;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:285:68: error: implicit instantiation of
>> undefined template 'std::pair<unsigned long, unsigned long>'
>> std::pair<const_iterator, const_iterator> p(expression() + pi.first,
>> expression() + pi.second);
>> ^
>> ./boost/detail/container_fwd.hpp:92:42: note: template is declared here
>> template <class T1, class T2> struct pair;
>> ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:527:9: error: too few template arguments
>> for class template 'basic_string'
>> std::basic_string<charT> BOOST_REGEX_CALL str()const
>> ^
>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared here
>> template <class charT, class traits, class Allocator> class
>> basic_string;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:67:
>> ./boost/regex/v4/basic_regex.hpp:529:52: error: too few template arguments
>> for class template 'basic_string'
>> return m_pimpl.get() ? m_pimpl->str() : std::basic_string<charT>();
>> ^
>> ./boost/detail/container_fwd.hpp:63:65: note: template is declared here
>> template <class charT, class traits, class Allocator> class
>> basic_string;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:70:
>> ./boost/regex/v4/basic_regex_creator.hpp:140:26: error: too few template
>> arguments for class template 'vector'
>> typedef typename std::vector<digraph_type>::const_iterator
>> list_iterator;
>> ^
>> ./boost/detail/container_fwd.hpp:82:47: note: template is declared here
>> template <class T, class Allocator> class vector;
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^
>> In file included from boost/regex/src/posix_api.cpp:22:
>> In file included from ./boost/regex.hpp:31:
>> In file included from ./boost/regex/v4/regex.hpp:70:
>> ./boost/regex/v4/basic_regex_creator.hpp:140:48: error: expected a qualified
>> name after 'typename'
>> typedef typename std::vector<digraph_type>::const_iterator
>> list_iterator;
>> ^
>> ./boost/regex/v4/basic_regex_creator.hpp:140:62: error: expected ';' at end
>> of declaration list
>> typedef typename std::vector<digraph_type>::const_iterator
>> list_iterator;
>> ^
>> ;
>> ./boost/regex/v4/basic_regex_creator.hpp:141:4: error: unknown type name
>> 'list_iterator'
>> list_iterator singles_begin()const
>> ^
>> fatal error: too many errors emitted, stopping now [-ferror-limit=]
>> 20 errors generated.
>>
>>
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