[Rcpp-devel] no matching function for call in mzR on Mac after Rcpp 0.11.0 update

[Dan Tenenbaum]

----- Original Message -----
> From: "Kevin Ushey" <kevinushey at gmail.com>
> To: "Steffen Neumann" <sneumann at ipb-halle.de>
> Cc: "rcpp-devel" <rcpp-devel at lists.r-forge.r-project.org>
> Sent: Friday, February 7, 2014 2:40:12 AM
> Subject: Re: [Rcpp-devel] no matching function for call in mzR on Mac after Rcpp 0.11.0 update
> 
> I will see if I can take a deeper look at this soon, but
> unfortunately, I do not have access to an older Mac machine. For
> reference, I am able to successfully compile and check mzR 1.9.3
> using
> Apple clang; however, I had to modify the Boost source included in
> the
> package a bit to get it to work. Some information for the interested
> follows...


As I mentioned to Steffen a couple of times, the issue is that the compiler used on the Bioconductor and CRAN build Macs is g++ 4.2.1; mzR does not build with that compiler. It builds under clang but changing compilers to accomodate this one package is not going to happen (long-term, both CRAN and Bioconductor will switch to clang/clang++ on Mac; we're following CRAN's lead and they have not made this move yet).

So the issue is figuring out what in mzR is too "new" for g++ 4.2.1.

Dan


> 
> In fact, Boost (that is, the subset packaged with mzR) is doing
> something illegal by trying to forward declare standard library
> containers in src/boost/detail/container_fwd.hpp, and this causes
> things to blow up for compilers using libc++. I have to remove the
> cruft and just keep the #include statements in order to successfully
> install the package. Ie, on package build I get the error:
> 
> clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB
> -D_NODEBUG
> -I/usr/local/include
> -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"
>   -fPIC  -g -O3 -march=native -pipe -Wall -pedantic -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;
>         ^
> with the packaged Boost as-is. Perhaps the define guard magic in
> boost/detail/container_fwd.hpp is not as robust as it should be.
> 
> Anyway, I'll see if there's something we can do to work around this
> tomorrow.
> 
> Cheers,
> Kevin
> 
> On Fri, Feb 7, 2014 at 12:42 AM, Steffen Neumann
> <sneumann at ipb-halle.de> wrote:
> > Hi list,
> >
> > sorry, it's me again.
> >
> > I am having issues to build mzR on Mac (to which I have no access)
> > after the upgrade to Rcpp 0.11.0 on both
> >
> > http://bioconductor.org/checkResults/2.13/bioc-LATEST/mzR/perceval-buildsrc.html
> > http://bioconductor.org/checkResults/2.14/bioc-LATEST/mzR/petty-buildsrc.html
> >
> > with the same error message on both machines. Other builds are
> > fine.
> > Those C++ error messages always scare the s**t out of me,
> > But then, the 100s of lines when a Java program throws
> > an exception are not better ...
> >
> > The following is what I understood. The problem occurs in the three
> > copy constructors
> > generated for the RcppRamp object in RcppRampModule.cpp[1]
> >
> >         Rcpp::S4_field<RcppRamp>::S4_field(const
> >         Rcpp::S4_field<RcppRamp>&),
> > and similar for
> >         S4_CppOverloadedMethods(const
> >         Rcpp::S4_CppOverloadedMethods<RcppRamp>&)
> > and     S4_CppConstructor(const
> > Rcpp::S4_CppConstructor<RcppRamp>&).
> >
> > In all cases, there is a call to
> > Reference_Impl<Rcpp::PreserveStorage>::Reference_Impl()
> > for which the compiler can't find a matching function. What it
> > offers are
> > implementations like Reference_Impl(const std::string&). The
> > difference is
> > that the requested Reference_Impl() comes with no arguments (?!).
> >
> > The call is made from Module.h:331 in the macro
> > RCPP_CTOR_ASSIGN(S4_field)
> > (Would it help to define RCPP_DEBUG for some additional output ?)
> > Indeed, all three "no matching function"s seem to come from this
> > macro:
> >
> >         grep RCPP_CTOR_ASSIGN ./include/Rcpp/*
> >         ./include/Rcpp/Module.h:
> >                RCPP_CTOR_ASSIGN(S4_CppConstructor)
> >         ./include/Rcpp/Module.h:
> >                RCPP_CTOR_ASSIGN(S4_CppOverloadedMethods)
> >         ./include/Rcpp/Module.h:        RCPP_CTOR_ASSIGN(S4_field)
> >
> > But unfortunately this is where I get lost. Since it works on other
> > architectures,
> > <wildGuess>
> > it could be that on Mac "something" is #defined to be an empty
> > string,
> > so that Reference_Impl() is called with an empty argument.
> > </wildGuess>
> >
> > <disclaimer>
> > Of course, my last ventures into C++-land is more than a decade
> > ago, so I could be waay off.
> > </disclaimer>
> >
> > Any ideas here ?
> >
> > Yours,
> > Steffen
> >
> > [1]
> > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/mzR/src/RcppRampModule.cpp
> >
> > -----------------------------------------------
> >
> > llvm-g++-4.2 -arch x86_64
> > -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG
> > -D_LARGEFILE_SOURCE -I./boost_aux/ -I. -DHAVE_PWIZ_MZML_LIB
> > -D_NODEBUG -I/usr/local/include
> > -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include"
> >   -fPIC  -mtune=core2 -g -O2  -c RcppRampModule.cpp -o
> > RcppRampModule.o
> >
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Module.h:
> > In copy constructor 'Rcpp::S4_field<Class>::S4_field(const
> > Rcpp::S4_field<Class>&) [with Class = RcppRamp]':
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/module/class.h:416:
> >   instantiated from 'Rcpp::List Rcpp::class_<Class>::fields(const
> > Rcpp::XPtr<Rcpp::class_Base, Rcpp::PreserveStorage, void
> > Rcpp::standard_delete_finalizer [with T = Rcpp::class_Base]>&)
> > [with Class = RcppRamp]'
> > RcppRampModule.cpp:22:   instantiated from here
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Module.h:331:
> > error: no matching function for call to
> > 'Rcpp::Reference_Impl<Rcpp::PreserveStorage>::Reference_Impl()'
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:56:
> > note: candidates are:
> > Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(const
> > std::string&) [with StoragePolicy = Rcpp::PreserveStorage]
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:41:
> > note:
> >                 Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(SEXPREC*)
> > [with StoragePolicy = Rcpp::PreserveStorage]
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:34:
> > note:
> >                 Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(const
> > Rcpp::Reference_Impl<StoragePolicy>&) [with StoragePolicy =
> > Rcpp::PreserveStorage]
> >
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Module.h:
> > In copy constructor
> > 'Rcpp::S4_CppOverloadedMethods<Class>::S4_CppOverloadedMethods(const
> > Rcpp::S4_CppOverloadedMethods<Class>&) [with Class = RcppRamp]':
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/module/class.h:435:
> >   instantiated from 'Rcpp::List
> > Rcpp::class_<Class>::getMethods(const Rcpp::XPtr<Rcpp::class_Base,
> > Rcpp::PreserveStorage, void Rcpp::standard_delete_finalizer [with
> > T = Rcpp::class_Base]>&, std::string&) [with Class = RcppRamp]'
> > RcppRampModule.cpp:22:   instantiated from here
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Module.h:256:
> > error: no matching function for call to
> > 'Rcpp::Reference_Impl<Rcpp::PreserveStorage>::Reference_Impl()'
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:56:
> > note: candidates are:
> > Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(const
> > std::string&) [with StoragePolicy = Rcpp::PreserveStorage]
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:41:
> > note:
> >                 Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(SEXPREC*)
> > [with StoragePolicy = Rcpp::PreserveStorage]
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:34:
> > note:
> >                 Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(const
> > Rcpp::Reference_Impl<StoragePolicy>&) [with StoragePolicy =
> > Rcpp::PreserveStorage]
> >
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Module.h:
> > In copy constructor
> > 'Rcpp::S4_CppConstructor<Class>::S4_CppConstructor(const
> > Rcpp::S4_CppConstructor<Class>&) [with Class = RcppRamp]':
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/module/class.h:446:
> >   instantiated from 'Rcpp::List
> > Rcpp::class_<Class>::getConstructors(const
> > Rcpp::XPtr<Rcpp::class_Base, Rcpp::PreserveStorage, void
> > Rcpp::standard_delete_finalizer [with T = Rcpp::class_Base]>&,
> > std::string&) [with Class = RcppRamp]'
> > RcppRampModule.cpp:22:   instantiated from here
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Module.h:218:
> > error: no matching function for call to
> > 'Rcpp::Reference_Impl<Rcpp::PreserveStorage>::Reference_Impl()'
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:56:
> > note: candidates are:
> > Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(const
> > std::string&) [with StoragePolicy = Rcpp::PreserveStorage]
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:41:
> > note:
> >                 Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(SEXPREC*)
> > [with StoragePolicy = Rcpp::PreserveStorage]
> > /Library/Frameworks/R.framework/Versions/3.1/Resources/library/Rcpp/include/Rcpp/Reference.h:34:
> > note:
> >                 Rcpp::Reference_Impl<StoragePolicy>::Reference_Impl(const
> > Rcpp::Reference_Impl<StoragePolicy>&) [with StoragePolicy =
> > Rcpp::PreserveStorage]
> >
> >
> > --
> > IPB Halle                    AG Massenspektrometrie & Bioinformatik
> > Dr. Steffen Neumann          http://www.IPB-Halle.DE
> > Weinberg 3                   http://msbi.bic-gh.de
> > 06120 Halle                  Tel. +49 (0) 345 5582 - 1470
> >                                   +49 (0) 345 5582 - 0
> > sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409
> >
> >
> >
> > _______________________________________________
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