[Rcpp-devel] no matching function for call in mzR on Mac after Rcpp 0.11.0 update
Kevin Ushey
kevinushey at gmail.com
Fri Feb 7 11:40:12 CET 2014
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...
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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