[Rcpp-devel] no matching function for call in mzR on Mac after Rcpp 0.11.0 update
Dan Tenenbaum
dtenenba at fhcrc.org
Fri Feb 7 20:40:09 CET 2014
Hi Kevin, all,
----- Original Message -----
> From: "Kevin Ushey" <kevinushey at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> Cc: "rcpp-devel" <rcpp-devel at lists.r-forge.r-project.org>, "Steffen Neumann" <sneumann at ipb-halle.de>
> Sent: Friday, February 7, 2014 10:50:03 AM
> Subject: Re: [Rcpp-devel] no matching function for call in mzR on Mac after Rcpp 0.11.0 update
>
> Hi everyone,
>
> I think I've gotten to the bottom of this. In Rcpp 0.10.6, the
> Rcpp::Reference classes defined a default constructor; this default
> constructor was left out in the reshuffle to Rcpp 0.11.0.
>
> I'm not as sure why, but newer compilers are either 1) automatically
> generating a default constructor, or 2) deciding one of the available
> constructors is still suitable. This does not happen with
> llvm-g++-4.2, hence the error.
>
Thanks very much for looking into this!
> I committed a hotfix to the installed version of Rcpp at BioC that
> should fix build problems for now; but we can decide what the
> appropriate solution in Rcpp is as well.
The way the BioC build system works is to download and build all dependencies anew every night, so the changes you made will not persist. So this means that if the problem is in Rcpp, then it needs to be solved in Rcpp and that solution needs to be pushed to CRAN. Until then, mzR and packages that depend on it will remain broken on mac.
So a swift solution in Rcpp and CRAN would be great.
Thanks!
Dan
>
> Cheers,
> Kevin
>
> On Fri, Feb 7, 2014 at 7:46 AM, Dan Tenenbaum <dtenenba at fhcrc.org>
> wrote:
> >
> >
> > ----- 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
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > Rcpp-devel mailing list
> >> > Rcpp-devel at lists.r-forge.r-project.org
> >> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> >> _______________________________________________
> >> Rcpp-devel mailing list
> >> Rcpp-devel at lists.r-forge.r-project.org
> >> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
> >>
>
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