Question: Issues while installing RBGL package
0
gravatar for jason tyler
6.3 years ago by
jason tyler10
jason tyler10 wrote:
Hi all, 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? [[alternative HTML version deleted]]
rbgl • 545 views
ADD COMMENTlink modified 6.3 years ago by Vincent J. Carey, Jr.6.3k • written 6.3 years ago by jason tyler10
Answer: Issues while installing RBGL package
0
gravatar for Vincent J. Carey, Jr.
6.3 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
please provide sessionInfo() and result of gcc -v On Tue, Feb 12, 2013 at 9:41 AM, jason tyler <mtyler.jason@gmail.com> wrote: > Hi all, > > 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<boos t::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? > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.3 years ago by Vincent J. Carey, Jr.6.3k
Answer: Issues while installing RBGL package
0
gravatar for Vincent J. Carey, Jr.
6.3 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
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 On Tue, Feb 12, 2013 at 8:47 PM, jason tyler <mtyler.jason@gmail.com> wrote: > *Results of gcc -v * > > 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 > > > > On Tue, Feb 12, 2013 at 8:19 PM, Vincent Carey <stvjc@channing.harvard.edu> > wrote: > >> please provide sessionInfo() and result of gcc -v >> >> On Tue, Feb 12, 2013 at 9:41 AM, jason tyler <mtyler.jason@gmail.com>wrote: >> >>> Hi all, >>> >>> 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<bo ost::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? >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> > [[alternative HTML version deleted]]
ADD COMMENTlink written 6.3 years ago by Vincent J. Carey, Jr.6.3k
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