[Rdkit-discuss] Compiling issues
Hi Greg, I have tried to install the latest RDKit on a freshly installed Ubuntu 10.10. After installing python-dev, sqlite3, numpy, bison, flex AND THE BOOST LIBRARIES VIA APT (boost 1.42), I additionally installed boost 1.4.2 in /opt/boost_1_42_0. During the cmake step flex and bison were found in /usr/lib. Several Warnings were issued during the cmake -DBOOST_ROOT=/opt/boost_1_42_0 .. -step. Obviously the system built boost installation was erroneously used (?is this the problem if the versions of boost are the same?). When doing the make the following error occurs: -snip [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o Linking CXX shared library ../../lib/libGraphMol.so [ 34%] Built target GraphMol [ 34%] [FLEX][SmartsL] Building scanner with flex /usr/bin/flex version 2.5.4 smarts.ll, line 1: unrecognized %option: reentrant smarts.ll, line 2: unrecognized %option: bison-bridge make[2]: *** [../Code/GraphMol/SmilesParse/lex.yysmarts.cpp] Error 1 make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] Error 2 make: *** [all] Error 2 -snip Here are my envs: -snip --mar...@markus:/opt/RDKit/build$ echo $RDBASE --/opt/RDKit --mar...@markus:/opt/RDKit/build$ echo $LD_LIBRARY_PATH --/opt/RDKit/lib:/opt/RDKit/bin:/opt/boost_1_42_0:/opt/boost_1_42_1/boost --mar...@markus:/opt/RDKit/build$ echo $PYTHONPATH --:/opt/RDKit:/opt/RDKit/rdkit -snip Does anyone have a hint? Thanks in advance, Markus -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compiling issues
HI Markus, On Mon, Nov 15, 2010 at 9:51 AM, Markus Kossner m.koss...@googlemail.com wrote: Hi Greg, I have tried to install the latest RDKit on a freshly installed Ubuntu 10.10. After installing python-dev, sqlite3, numpy, bison, flex AND THE BOOST LIBRARIES VIA APT (boost 1.42), I additionally installed boost 1.4.2 in /opt/boost_1_42_0. During the cmake step flex and bison were found in /usr/lib. Several Warnings were issued during the cmake -DBOOST_ROOT=/opt/boost_1_42_0 .. -step. Obviously the system built boost installation was erroneously used (?is this the problem if the versions of boost are the same?). Should be no problem. In fact, if the system boost is the version you want, then you shouldn't need to install your own at all. When doing the make the following error occurs: -snip [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o Linking CXX shared library ../../lib/libGraphMol.so [ 34%] Built target GraphMol [ 34%] [FLEX][SmartsL] Building scanner with flex /usr/bin/flex version 2.5.4 smarts.ll, line 1: unrecognized %option: reentrant smarts.ll, line 2: unrecognized %option: bison-bridge make[2]: *** [../Code/GraphMol/SmilesParse/lex.yysmarts.cpp] Error 1 make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] Error 2 make: *** [all] Error 2 -snip This is almost definitely due to an older version of flex. There's some info here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01079.html From what I can tell about Ubuntu 10.10, you should have a more recent version of flex available... did you install the flex-old package? Best Regards, -greg -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compiling issues
Hi Greg, exactly that was the case. RDKit nicely installs now! Cheers, Markus On 11/15/2010 10:05 AM, Greg Landrum wrote: HI Markus, On Mon, Nov 15, 2010 at 9:51 AM, Markus Kossner m.koss...@googlemail.com wrote: Hi Greg, I have tried to install the latest RDKit on a freshly installed Ubuntu 10.10. After installing python-dev, sqlite3, numpy, bison, flex AND THE BOOST LIBRARIES VIA APT (boost 1.42), I additionally installed boost 1.4.2 in /opt/boost_1_42_0. During the cmake step flex and bison were found in /usr/lib. Several Warnings were issued during the cmake -DBOOST_ROOT=/opt/boost_1_42_0 .. -step. Obviously the system built boost installation was erroneously used (?is this the problem if the versions of boost are the same?). Should be no problem. In fact, if the system boost is the version you want, then you shouldn't need to install your own at all. When doing the make the following error occurs: -snip [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o [ 34%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o Linking CXX shared library ../../lib/libGraphMol.so [ 34%] Built target GraphMol [ 34%] [FLEX][SmartsL] Building scanner with flex /usr/bin/flex version 2.5.4 smarts.ll, line 1: unrecognized %option: reentrant smarts.ll, line 2: unrecognized %option: bison-bridge make[2]: *** [../Code/GraphMol/SmilesParse/lex.yysmarts.cpp] Error 1 make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all] Error 2 make: *** [all] Error 2 -snip This is almost definitely due to an older version of flex. There's some info here: http://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg01079.html From what I can tell about Ubuntu 10.10, you should have a more recent version of flex available... did you install the flex-old package? Best Regards, -greg -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Building RDKit on CentOS 5
I've been working to build RDKit on Centos 5, and I'm hitting a very common error. Unfortunately, none of the standard fixes have helped. Details: The error that I'm seeing is this: [ 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/../lib64/libboost_regex.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/../lib64/libboost_regex.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 I've taken the standard steps of building Python (v2.7) with the -fPIC flag. Specficially, I attached CFLAGS=-fPIC to configure in the Python build. This solved the first instance of this type of error occuring at about 3%. I've also tried the two fixes for Boost with the following command line to build RDKit: cmake -DBOOST_ROOT=/usr/local -DBoost_USE_STATIC_LIBS=OFF .. I still get this error, and I notice that the Boost libraries that are being referred to are actually the system installation in usr/lib64 and not those that I've build in /usr/local/lib. It would seem that I can't seem to force make to look in the right location. Any tips are greatly apprciated. -Kirk -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on CentOS 5
Have you tried to remove the CMake cache file before rerun cmake? rm -f CMakeCache.txt After rerun cmake, take a look at that file again and make sure things like Boost_INCLUDE_DIR and Boost_LIBRARY_DIRS all point to /usr/local/include and /usr/local/lib, etc. Eddie On Nov 15, 2010, at 12:45 PM, Robert DeLisle wrote: I've been working to build RDKit on Centos 5, and I'm hitting a very common error. Unfortunately, none of the standard fixes have helped. Details: The error that I'm seeing is this: [ 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/../lib64/libboost_regex.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/../lib64/libboost_regex.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 I've taken the standard steps of building Python (v2.7) with the -fPIC flag. Specficially, I attached CFLAGS=-fPIC to configure in the Python build. This solved the first instance of this type of error occuring at about 3%. I've also tried the two fixes for Boost with the following command line to build RDKit: cmake -DBOOST_ROOT=/usr/local -DBoost_USE_STATIC_LIBS=OFF .. I still get this error, and I notice that the Boost libraries that are being referred to are actually the system installation in usr/lib64 and not those that I've build in /usr/local/lib. It would seem that I can't seem to force make to look in the right location. Any tips are greatly apprciated. -Kirk -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on CentOS 5
Yep, I've defintely done that. I've even gone so far as to wipe out the directory entirely and start with a fresh RDKit directory. I also looked into the cache file and seen that the library directories appear to be set as /usr/local/lib and /user/local/lib64, but one the error occurs, it refers to /usr/lib64. I can't seem to find any reason for this. -Kirk On Mon, Nov 15, 2010 at 3:26 PM, Eddie Cao cao.yi...@gmail.com wrote: Have you tried to remove the CMake cache file before rerun cmake? rm -f CMakeCache.txt After rerun cmake, take a look at that file again and make sure things like Boost_INCLUDE_DIR and Boost_LIBRARY_DIRS all point to /usr/local/include and /usr/local/lib, etc. Eddie On Nov 15, 2010, at 12:45 PM, Robert DeLisle wrote: I've been working to build RDKit on Centos 5, and I'm hitting a very common error. Unfortunately, none of the standard fixes have helped. Details: The error that I'm seeing is this: [ 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/../lib64/libboost_regex.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/../lib64/libboost_regex.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 I've taken the standard steps of building Python (v2.7) with the -fPIC flag. Specficially, I attached CFLAGS=-fPIC to configure in the Python build. This solved the first instance of this type of error occuring at about 3%. I've also tried the two fixes for Boost with the following command line to build RDKit: cmake -DBOOST_ROOT=/usr/local -DBoost_USE_STATIC_LIBS=OFF .. I still get this error, and I notice that the Boost libraries that are being referred to are actually the system installation in usr/lib64 and not those that I've build in /usr/local/lib. It would seem that I can't seem to force make to look in the right location. Any tips are greatly apprciated. -Kirk -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on CentOS 5
It must be something in the release version of RDKit. I just grabbed the SVN version, put it in the same location, followed the same procedures, and it has just compiled fine without any other changes on my part. Greg - any ideas what the difference is here? Not that it matters given that the SVN is working, but just for curiosity's sake. Sadly, now I get this from with Python: from rdkit import Chem Traceback (most recent call last): File stdin, line 1, in module File /opt/RDKit_svn_20101115/rdkit/Chem/__init__.py, line 18, in module from rdkit import rdBase ImportError: /usr/lib64/libboost_python.so.2: undefined symbol: PyUnicodeUCS4_FromEncodedObject -Kirk On Mon, Nov 15, 2010 at 3:28 PM, Robert DeLisle rkdeli...@gmail.com wrote: Yep, I've defintely done that. I've even gone so far as to wipe out the directory entirely and start with a fresh RDKit directory. I also looked into the cache file and seen that the library directories appear to be set as /usr/local/lib and /user/local/lib64, but one the error occurs, it refers to /usr/lib64. I can't seem to find any reason for this. -Kirk On Mon, Nov 15, 2010 at 3:26 PM, Eddie Cao cao.yi...@gmail.com wrote: Have you tried to remove the CMake cache file before rerun cmake? rm -f CMakeCache.txt After rerun cmake, take a look at that file again and make sure things like Boost_INCLUDE_DIR and Boost_LIBRARY_DIRS all point to /usr/local/include and /usr/local/lib, etc. Eddie On Nov 15, 2010, at 12:45 PM, Robert DeLisle wrote: I've been working to build RDKit on Centos 5, and I'm hitting a very common error. Unfortunately, none of the standard fixes have helped. Details: The error that I'm seeing is this: [ 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/../lib64/libboost_regex.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/../lib64/libboost_regex.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 I've taken the standard steps of building Python (v2.7) with the -fPIC flag. Specficially, I attached CFLAGS=-fPIC to configure in the Python build. This solved the first instance of this type of error occuring at about 3%. I've also tried the two fixes for Boost with the following command line to build RDKit: cmake -DBOOST_ROOT=/usr/local -DBoost_USE_STATIC_LIBS=OFF .. I still get this error, and I notice that the Boost libraries that are being referred to are actually the system installation in usr/lib64 and not those that I've build in /usr/local/lib. It would seem that I can't seem to force make to look in the right location. Any tips are greatly apprciated. -Kirk -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on CentOS 5
Make sure /usr/local/lib appears before /usr/lib64 in your LD_LIBRARY_PATH. It seems python import loads the system boost rather than your custom boost. -Eddie On Nov 15, 2010, at 2:44 PM, Robert DeLisle wrote: It must be something in the release version of RDKit. I just grabbed the SVN version, put it in the same location, followed the same procedures, and it has just compiled fine without any other changes on my part. Greg - any ideas what the difference is here? Not that it matters given that the SVN is working, but just for curiosity's sake. Sadly, now I get this from with Python: from rdkit import Chem Traceback (most recent call last): File stdin, line 1, in module File /opt/RDKit_svn_20101115/rdkit/Chem/__init__.py, line 18, in module from rdkit import rdBase ImportError: /usr/lib64/libboost_python.so.2: undefined symbol: PyUnicodeUCS4_FromEncodedObject -Kirk On Mon, Nov 15, 2010 at 3:28 PM, Robert DeLisle rkdeli...@gmail.com wrote: Yep, I've defintely done that. I've even gone so far as to wipe out the directory entirely and start with a fresh RDKit directory. I also looked into the cache file and seen that the library directories appear to be set as /usr/local/lib and /user/local/lib64, but one the error occurs, it refers to /usr/lib64. I can't seem to find any reason for this. -Kirk On Mon, Nov 15, 2010 at 3:26 PM, Eddie Cao cao.yi...@gmail.com wrote: Have you tried to remove the CMake cache file before rerun cmake? rm -f CMakeCache.txt After rerun cmake, take a look at that file again and make sure things like Boost_INCLUDE_DIR and Boost_LIBRARY_DIRS all point to /usr/local/include and /usr/local/lib, etc. Eddie On Nov 15, 2010, at 12:45 PM, Robert DeLisle wrote: I've been working to build RDKit on Centos 5, and I'm hitting a very common error. Unfortunately, none of the standard fixes have helped. Details: The error that I'm seeing is this: [ 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/../lib64/libboost_regex.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/../lib64/libboost_regex.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 I've taken the standard steps of building Python (v2.7) with the -fPIC flag. Specficially, I attached CFLAGS=-fPIC to configure in the Python build. This solved the first instance of this type of error occuring at about 3%. I've also tried the two fixes for Boost with the following command line to build RDKit: cmake -DBOOST_ROOT=/usr/local -DBoost_USE_STATIC_LIBS=OFF .. I still get this error, and I notice that the Boost libraries that are being referred to are actually the system installation in usr/lib64 and not those that I've build in /usr/local/lib. It would seem that I can't seem to force make to look in the right location. Any tips are greatly apprciated. -Kirk -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on CentOS 5
Yes, that is also true. The error in my most recent messages stems from the default build of Python supporst Unicode UCS2, but apparently boost expects UCS4. A rebuild of Python with UCS4 enabled fixed that problem. Now I get a similar error related to Py_InitModule4 not being defined. From what I can find, this is a 32-bit - 64-bit problem in which this was defined as Py_InitModule4_64 in the 64-bit Python libraries but that change may not have cascaded to all necessary parts of the build process. Most of the changes involve some substantial changes to the accessing code, but I'm still looking for a better option. On Mon, Nov 15, 2010 at 4:14 PM, Eddie Cao cao.yi...@gmail.com wrote: Make sure /usr/local/lib appears before /usr/lib64 in your LD_LIBRARY_PATH. It seems python import loads the system boost rather than your custom boost. -Eddie On Nov 15, 2010, at 2:44 PM, Robert DeLisle wrote: It must be something in the release version of RDKit. I just grabbed the SVN version, put it in the same location, followed the same procedures, and it has just compiled fine without any other changes on my part. Greg - any ideas what the difference is here? Not that it matters given that the SVN is working, but just for curiosity's sake. Sadly, now I get this from with Python: from rdkit import Chem Traceback (most recent call last): File stdin, line 1, in module File /opt/RDKit_svn_20101115/rdkit/Chem/__init__.py, line 18, in module from rdkit import rdBase ImportError: /usr/lib64/libboost_python.so.2: undefined symbol: PyUnicodeUCS4_FromEncodedObject -Kirk On Mon, Nov 15, 2010 at 3:28 PM, Robert DeLisle rkdeli...@gmail.comwrote: Yep, I've defintely done that. I've even gone so far as to wipe out the directory entirely and start with a fresh RDKit directory. I also looked into the cache file and seen that the library directories appear to be set as /usr/local/lib and /user/local/lib64, but one the error occurs, it refers to /usr/lib64. I can't seem to find any reason for this. -Kirk On Mon, Nov 15, 2010 at 3:26 PM, Eddie Cao cao.yi...@gmail.com wrote: Have you tried to remove the CMake cache file before rerun cmake? rm -f CMakeCache.txt After rerun cmake, take a look at that file again and make sure things like Boost_INCLUDE_DIR and Boost_LIBRARY_DIRS all point to /usr/local/include and /usr/local/lib, etc. Eddie On Nov 15, 2010, at 12:45 PM, Robert DeLisle wrote: I've been working to build RDKit on Centos 5, and I'm hitting a very common error. Unfortunately, none of the standard fixes have helped. Details: The error that I'm seeing is this: [ 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/../lib64/libboost_regex.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/../lib64/libboost_regex.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 I've taken the standard steps of building Python (v2.7) with the -fPIC flag. Specficially, I attached CFLAGS=-fPIC to configure in the Python build. This solved the first instance of this type of error occuring at about 3%. I've also tried the two fixes for Boost with the following command line to build RDKit: cmake -DBOOST_ROOT=/usr/local -DBoost_USE_STATIC_LIBS=OFF .. I still get this error, and I notice that the Boost libraries that are being referred to are actually the system installation in usr/lib64 and not those that I've build in /usr/local/lib. It would seem that I can't seem to force make to look in the right location. Any tips are greatly apprciated. -Kirk -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net
Re: [Rdkit-discuss] Building RDKit on CentOS 5
Hi Kirk, On Mon, Nov 15, 2010 at 11:44 PM, Robert DeLisle rkdeli...@gmail.com wrote: It must be something in the release version of RDKit. I just grabbed the SVN version, put it in the same location, followed the same procedures, and it has just compiled fine without any other changes on my part. Greg - any ideas what the difference is here? Not that it matters given that the SVN is working, but just for curiosity's sake. I'm afraid I don't really know why there would be a difference. I can't think of anything that has changed between the release and now that would cause this behavior. -greg -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on CentOS 5
Kirk, On Tue, Nov 16, 2010 at 12:38 AM, Robert DeLisle rkdeli...@gmail.com wrote: Yes, that is also true. The error in my most recent messages stems from the default build of Python supporst Unicode UCS2, but apparently boost expects UCS4. A rebuild of Python with UCS4 enabled fixed that problem. Now I get a similar error related to Py_InitModule4 not being defined. From what I can find, this is a 32-bit - 64-bit problem in which this was defined as Py_InitModule4_64 in the 64-bit Python libraries but that change may not have cascaded to all necessary parts of the build process. Most of the changes involve some substantial changes to the accessing code, but I'm still looking for a better option. Could it be that the boost libraries you are using were not built in 64bit mode? I've managed to force a 64bit build in the past with the following command line: ./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install Best Regards, -greg -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Building RDKit on CentOS 5
No, I made sure to include the address-model=64 switch to bjam. Tomorrow when I get in I'll update the thread with all the steps I've followed. -Kirk On Nov 15, 2010 9:52pm, Greg Landrum greg.land...@gmail.com wrote: Kirk, On Tue, Nov 16, 2010 at 12:38 AM, Robert DeLisle rkdeli...@gmail.com wrote: Yes, that is also true. The error in my most recent messages stems from the default build of Python supporst Unicode UCS2, but apparently boost expects UCS4. A rebuild of Python with UCS4 enabled fixed that problem. Now I get a similar error related to Py_InitModule4 not being defined. From what I can find, this is a 32-bit - 64-bit problem in which this was defined as Py_InitModule4_64 in the 64-bit Python libraries but that change may not have cascaded to all necessary parts of the build process. Most of the changes involve some substantial changes to the accessing code, but I'm still looking for a better option. Could it be that the boost libraries you are using were not built in 64bit mode? I've managed to force a 64bit build in the past with the following command line: ./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install Best Regards, -greg -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
