[Rcppoctave-user] Apple Blues

[Renaud Gaujoux]

---------- Forwarded message ----------
From: Dominick Samperi <djsamperi at gmail.com>
Date: 30 October 2013 18:04
Subject: Re: Apple Blues
To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za>


I built R using clang/clang++/gfortran-4.2(from Simon of R core) and
installed Rcpp using the same tools, and
there were no obvious problems.

There was a problem with RcppOctave/src/modules/Makefile.in.
I've attached my work-around.

When I try to install RcppOctave with Octave 3.6.4
I get the familiar issue:

clang++ -arch x86_64 -std=c++11
-I/Users/dsamperi/bin/R-clang/R.framework/Resources/include -DNDEBUG
`"/Users/dsamperi/bin/R-clang/R.framework/Resources/bin/Rscript" -e
"Rcpp:::CxxFlags()"` -DOCT_POST_3_4_0=1
-I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave"
-I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/../"
-I"/usr/local/Cellar/octave/3.6.4/include/octave-3.6.4/octave/octave"
-I/usr/local/include
-I"/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/include"
  -fPIC  -g -O2  -c rcpp_octave.cpp -o rcpp_octave.o
clang++ -arch x86_64 -std=c++11 -dynamiclib
-Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module
-multiply_defined suppress -L/usr/local/lib -o RcppOctave.so conversion.o
rcpp_octave.o
/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/Rcpp/lib/libRcpp.a
-L/usr/local/Cellar/octave/3.6.4/lib/octave/3.6.4
-L/usr/local/Cellar/octave/3.6.4/lib -loctinterp -loctave -lcruft
-F/Users/dsamperi/bin/R-clang/R.framework/.. -framework R -Wl,-framework
-Wl,CoreFoundation
installing to
/Users/dsamperi/bin/R-clang/R.framework/Versions/3.0/Resources/library/RcppOctave/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
R(45582) malloc: *** error for object 0x1058257c0: pointer being freed was
not allocated
*** set a breakpoint in malloc_error_break to debug
/Users/dsamperi/bin/R-clang/R.framework/Resources/bin/INSTALL: line 34:
45581 Done                    echo 'tools:::.install_packages()'
     45582 Abort trap: 6           | R_DEFAULT_PACKAGES= LC_COLLATE=C
"${R_HOME}/bin/R" $myArgs --slave --args ${args}


On Wed, Oct 30, 2013 at 1:32 AM, Dominick Samperi <djsamperi at gmail.com>wrote:

> A little more searching revealed that llvm-g++
> and llvm-gcc are part of LLVM releases 2.9 and
> earlier, see...
> http://llvm.org/releases/download.html#3.3
>
> It seems like Mac OS X users of R will have to
> use a specific toolchain for all apps that need to
> link against each other, and this is especially true
> for RcppOctave…
>
> And the easiest toolchain to use under Mac OS X is
> the one specified by Apple! (Unfortunately this does
> not solve the Fortran problem.)
>
>
>
> On Wed, Oct 30, 2013 at 1:11 AM, Dominick Samperi <djsamperi at gmail.com>wrote:
>
>> Hello Renaud,
>>
>> I just tried unsuccessfully to upgrade my Apple desktop to
>> Mac OS X 10.9 (Mavericks), but due to a few technical
>> problems I had to backtrack to the previous version
>> 10.8 for now.
>>
>> After restoring from backups and checking
>> that everything works, I discovered that RcppOctave
>> does not install. I get the same invalid malloc error that
>> I was getting before. But this time I have not used
>> MacPorts at all, only Homebrew, and the version of
>> Octave is 3.6.4 as it should be.
>>
>> (I am downloading source, not using install.packages(), because
>> the latter tends to download old archives.)
>>
>> Indeed, with my fresh install of Mac OS X, with the
>> command line tools and Xcode installed, R does not
>> issue the correct command: R CMD config CXX
>> returns: llvm-g++-4.2 -arch x86_64.
>>
>> But there is no llvm-g++-4.2, only /usr/bin/g++ (version
>> 4.2.1) and /usr/bin/gcc (version 4.2.1). I tried to work-around
>> this problem by defining symbolic links llvm-g++-4.2 and
>> llvm-gcc-4.2 pointing to these files, but this does not work.
>>
>> There are a couple of open issues:
>> 1. Apple no longer ships binaries named llvm-g++-4.2 and
>>    llvm-gcc-4.2 (only g++ and gcc).
>> 2. Apple no longer supports Fortran at all (the R core team
>>     provides gfortran-4.2…see R Mac OS FAQ).
>> 3. 'brew install octave' does not show you what it is doing,
>>    and I think it may be using clang instead of gcc, clang++
>>    instead of g++.
>> 4. The segfault error when I try to install RcppOctave is
>>     probably due to compiler version incompatibilities, either
>>     gcc-4.2 vs gcc-4.2.1, or more likely, gcc-4.2.1 vs clang, etc.
>>
>> Thus under Mac OS X the correct long-term solution is to
>> stop using gcc/g++ and follow Apple in using clang/clang++.
>> In the mean time, Apple will make life difficult for people who
>> continue to use gcc/g++/gfortran! (There is an open source
>> project to write an LLVM Fortran front-end, but I don't know
>> what the status of that project is.)
>>
>> Dominick
>>
>>
>
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