Jason,
that looks like an interaction of clang with the Boost version inside RBGL - as
the error shows it re-defines "p" as an enum type which means anything
named p will be broken. Try using g++ instead of clang, I would hope that should
be more successful.
Cheers,
S
On Feb 22, 2013, at 5:26 PM, jason tyler wrote:
> Hi all,
>
> I was installing a package *RBGL* of bioconductor. However, I had some
> issues while installing it. I asked the devel group of bioconductor and
> they told me to consult this group. Here is my conversation with the
> bioconductor group related to the problem
>
>
> *Me->*
> I was trying to install the RBGL package using the following command
>
> biocLite("RBGL")
>
> However, I got the following error
> *
> installing *source* package ?RBGL? ...
> untarring boost include tree...
> ** libs
> /usr/bin/clang++ -I/usr/local/Cellar/r/2.15.1/R.framework/Resources/include
> -DNDEBUG -I/usr/local/Cellar/readline/6.2.4/include -isystem
> /usr/local/include -I/usr/X11/include -Irbgl_trimmed_boost_1_49_0 -fPIC
> -Os -w -pipe -march=native -Qunused-arguments -mmacosx-version-min=10.7 -c
> bbc.cpp -o bbc.o
> /usr/bin/clang++ -I/usr/local/Cellar/r/2.15.1/R.framework/Resources/include
> -DNDEBUG -I/usr/local/Cellar/readline/6.2.4/include -isystem
> /usr/local/include -I/usr/X11/include -Irbgl_trimmed_boost_1_49_0 -fPIC
> -Os -w -pipe -march=native -Qunused-arguments -mmacosx-version-min=10.7 -c
> cliques.cpp -o cliques.o
> cliques.cpp:26:31: error: redefinition of 'p' as different kind of
symbol
> std::pair<Edge, bool> p;
> ^
> rbgl_trimmed_boost_1_49_0/boost/mpl/assert.hpp:149:42: note: previous
> definition is here
> BOOST_MPL_AUX_ASSERT_CONSTANT( bool, p = !p_type::value );
> ^
> rbgl_trimmed_boost_1_49_0/boost/mpl/assert.hpp:56:58: note: expanded from
> macro 'BOOST_MPL_AUX_ASSERT_CONSTANT'
> # define BOOST_MPL_AUX_ASSERT_CONSTANT(T, expr) enum { expr }
> ^
> cliques.cpp:53:19: error: expression is not assignable
> p = edge(*va1, *va2, g);
> ~ ^
> cliques.cpp:54:25: error: member reference base type
>
'mpl_::assert_arg_pred_not<boost::detail::is_iterator_traversal<boost::random_access_traversal_tag>>::<anonymous
> enum at
> rbgl_trimmed_boost_1_49_0/boost/mpl/assert.hpp:149:5>' is not a
> structure or union
> if ( !p.second ) return FALSE;*
>
>
> Any suggestions how to overcome this or what is causing this issue?
>
> *Vincent Gray(of bioconductor group) -> *
> please provide sessionInfo() and result of gcc -v
>
> *Me->*
> gcc -v
> Using built-in specs.
> Target: i686-apple-darwin11
> Configured with:
> /private/var/tmp/llvmgcc42/llvmgcc42-2336.11~28/src/configure
> --disable-checking --enable-werror
> --prefix=/Applications/Xcode.app/Contents/Developer/usr/llvm-gcc-4.2
> --mandir=/share/man --enable-languages=c,objc,c++,obj-c++
> --program-prefix=llvm- --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/
> --with-slibdir=/usr/lib --build=i686-apple-darwin11
>
--enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.11~28/dst-llvmCore/Developer/usr/local
> --program-prefix=i686-apple-darwin11- --host=x86_64-apple-darwin11
> --target=i686-apple-darwin11 --with-gxx-include-dir=/usr/include/c++/4.2.1
> Thread model: posix
> gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
>
>
> *sessionInfo() Results*
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin11.4.0 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.1
>
> Thanks
>
> Regards,
> Jason
>
> *Vincent Gray -> *
> OK, I didn't read your log too well, so I missed that you are using
> clang++. Theoretically it will work
>
> http://blog.llvm.org/2010/05/clang-builds-boost.html
>
> I am using the gcc supplied in Xcode 4.0.2, with
>
> bash-3.2$ gcc -v
> Using built-in specs.
> Target: i686-apple-darwin10
> Configured with: /var/tmp/gcc/gcc-5666.3~123/src/configure
> --disable-checking --enable-werror --prefix=/usr --mandir=/share/man
> --enable-languages=c,objc,c++,obj-c++
> --program-transform-name=/^[cg][^.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib
> --build=i686-apple-darwin10 --program-prefix=i686-apple-darwin10-
> --host=x86_64-apple-darwin10 --target=i686-apple-darwin10
> --with-gxx-include-dir=/include/c++/4.2.1
> Thread model: posix
> gcc version 4.2.1 (Apple Inc. build 5666) (dot 3)
>
> this has no problem installing RBGL from source. your R is a little out of
> date but I don't think that's an issue.
>
> I have minimal experience with clang++ and you may have to take this to
> R-help or R-devel if you are not going to use Xcode- based compilation, as
> that's what we are basing our builds/tests on. I did try
>
> bash-3.2$ clang++ -v
> clang version 3.2 (tags/RELEASE_32/final)
> Target: x86_64-apple-darwin10.8.0
> Thread model: posix
> bash-3.2$ clang++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names
> -undefined dynamic_lookup -single_module -multiply_defined suppress
> -L/Users/stvjc/ExternalSoft/READLINE-62-DIST/lib -lreadline
> -L//Users/stvjc/ExternalSoft/LIBICONV-64/lib -liconv
> -L/Users/stvjc/ExternalSoft/jpeg-6b -ljpeg -o cliques.so cliques.o
> -F/Users/stvjc/ExternalSoft/R-devel-dist/R.framework/.. -framework R
> -Wl,-framework -Wl,CoreFoundation
>
> and this aping of the R CMD SHLIB command with clang++ quietly produced a
> .so. Upon linking this in, example(maxClique) worked. I am not too
> confident that this proves anything. But perhaps you need to update
> clang++?
>
>> sessionInfo()
> R version 2.15.2 Patched (2012-12-18 r61368)
> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit)
>
> locale:
> [1]
>
en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII
>
> attached base packages:
> [1] stats graphics grDevices datasets utils tools methods
> [8] base
>
> other attached packages:
> [1] BiocInstaller_1.8.3 weaver_1.24.0 codetools_0.2-8
> [4] digest_0.6.0
>
>
> *It's been weeks and I haven't been able to install it. Any
suggestions
> will be highly appreciated. Thanks group*
>
> Regards,
> Jason
>
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>
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