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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