[Rdkit-discuss] problem compiling RDKit_Q22010_1
Hi, I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64 ... [ 82%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o [ 83%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o [ 83%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o [ 84%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o Linking CXX shared library libSLNParse.so /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a(instances.o): relocation R_X86_64_32 against `boost::object_cacheboost::re_detail::cpp_regex_traits_basechar, boost::re_detail::cpp_regex_traits_implementationchar ::do_get(boost::re_detail::cpp_regex_traits_basechar const, unsigned long)::s_data' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1 make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2 make: *** [all] Error 2 Is this something known or should I start digging? Is this the right thing to compile or should I be using the svn repo version? Cheers, Paul. -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] problem compiling RDKit_Q22010_1
Hi Paul, On Wed, Aug 25, 2010 at 4:26 PM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: Hi, I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64 snip Linking CXX shared library libSLNParse.so /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a(instances.o): relocation R_X86_64_32 against `boost::object_cacheboost::re_detail::cpp_regex_traits_basechar, boost::re_detail::cpp_regex_traits_implementationchar ::do_get(boost::re_detail::cpp_regex_traits_basechar const, unsigned long)::s_data' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a: could not read symbols: Bad value collect2: ld returned 1 exit status I never compiled rdkit on that distribution, but it looks like you encountered one of the Frequently Encountered Problems documented at the end of this wiki page: http://code.google.com/p/rdkit/wiki/BuildingWithCmake The suggested fix is: Add this to the arguments when you call cmake: -DBoost_USE_STATIC_LIBS=OFF Hope that helps, Riccardo -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] problem compiling RDKit_Q22010_1
Hi Paul, On Wed, Aug 25, 2010 at 7:26 AM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: Hi, I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64 ... unsigned long)::s_data' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1 make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2 make: *** [all] Error 2 Is this something known or should I start digging? There's information about this problem (and a solution) towards the bottom here: http://code.google.com/p/rdkit/wiki/BuildingWithCmake and in this thread: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01119.html I've also made some changes in svn so that the situation doesn't occur if you are willing to use a non-release version of the code. -greg -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] problem compiling RDKit_Q22010_1
On 25/08/10 16:14, Greg Landrum wrote: Hi Paul, On Wed, Aug 25, 2010 at 7:26 AM, Paul Emsleypaul.ems...@bioch.ox.ac.uk wrote: Hi, I am trying to compile RDKit for the first time, ubuntu 10.04 x86_64 ... unsigned long)::s_data' can not be used when making a shared object; recompile with -fPIC /usr/lib/gcc/x86_64-linux-gnu/4.4.3/../../../../lib/libboost_regex-mt.a: could not read symbols: Bad value collect2: ld returned 1 exit status make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Error 1 make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Error 2 make: *** [all] Error 2 Is this something known or should I start digging? There's information about this problem (and a solution) towards the bottom here: http://code.google.com/p/rdkit/wiki/BuildingWithCmake and in this thread: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01119.html I've also made some changes in svn so that the situation doesn't occur if you are willing to use a non-release version of the code. Hi Greg and Riccardo, Thanks for your prompt replies. I re-ran cmake with -DBoost_USE_STATIC_LIBS=OFF, however, it still failed at the same place. I checked out the latest revision and that compiles cleanly. Thanks, Paul. -- Sell apps to millions through the Intel(R) Atom(Tm) Developer Program Be part of this innovative community and reach millions of netbook users worldwide. Take advantage of special opportunities to increase revenue and speed time-to-market. Join now, and jumpstart your future. http://p.sf.net/sfu/intel-atom-d2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
