Re: [Rdkit-discuss] Problem building recent revisions on Windows
On Wed, Apr 8, 2015 at 6:41 PM, Greg Landrum greg.land...@gmail.com wrote: That's the second pointer to appveyor on this topic. Time for me to investigate. It would be awesome to have this happen automatically like with the linux builds on Travis. Just a followup to the list on what's going on here: I spent some time yesterday and today looking into setting up automated Windows builds/tests for the RDKit with Appveyor. It looks like a solid system and it was quite easy to figure out, but it turns out that RDKit builds are just too resource intensive for the system. Even with most of the features (like the Python and Java wrappers) turned off, all the builds I tried ended up failing because they took more than 40 minutes to complete. I will keep my eyes open for other options and would be happy to hear other suggestions if anyone has any. -greg -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Thanks Greg I have now tried using boost 1.56 (the cmake configuration once BOOST_ROOT is set is a little different vs. 1.55…). Either way I can’t seem to build with threadsafe/multithreaded support – but perhaps we should draw a line under it for now / follow-up ‘off-line’(?). The good news is that (with the thread settings OFF) the changes you checked-in (rev5616) have indeed sorted the MolHash piece, and all tests pass – thanks! Kind regards James From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 14 April 2015 05:35 To: James Davidson Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Problem building recent revisions on Windows Hi James Thanks for your patience here. I will invest the time in trying to get automated builds happening on this Windows side so that this stops happening. I just pushed some changes that should clear up the MolHash-related build problems. I had forgotten that that bit of code still needed to be tested on Windows. I haven't tested building the cartridge on Windows (I'm not set up to do that), but the python wrappers definitely do build for me now with both RDK_BUILD_THREADSAFE_SSS and RDK_TEST_MULTITHREADED set to ON. I don't think it should make a difference, but just in case: I am doing this using boost 1.56. Best, -greg On Mon, Apr 13, 2015 at 11:30 AM, James Davidson j.david...@vernalis.commailto:j.david...@vernalis.com wrote: Here’s an update: Tried building rev5211, but saw similar linking errors (to do with Boost threading libraries). The most recent build that I have successfully managed without the errors is rev5016. It occurred to me that a couple of my cmake options relate to threading (RDK_BUILD_THREADSAFE=ON; RDK_TEST_MULTITHREADED=ON) – and perhaps other people (Greg, Paolo) with successful Windows builds had these set OFF (default)(?). Indeed, if I set both of these to OFF, I can successfully build rev5211, and all of the tests pass. So this is good – but I still don’t understand what has changed (in relation to Boost threading) that means that later versions don’t build… Threading aside, I was now feeling pretty confident that I would be ok to build the latest revision (rev5611). Unfortunately this was not the case – I initially hit a problem with MolHash.cpp, which I thought was down to MSVC being stupid about snprintf() (line 265). After a little stack-overflowing, I thought changing this to _snprintf() would solve the problem – which it appears to (at least MolHash.cpp now compiles), but then I get a couple of further errors down-stream (probably related to the change I made?): Error 1 error LNK2019: unresolved external symbol class std::basic_stringchar,struct std::char_traitschar,class std::allocatorchar __cdecl RDKit::Descriptors::calcMolFormula(class RDKit::ROMol const ,bool,bool) (?calcMolFormula@Descriptors@RDKit@@YA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@AEBVROMol@2@_N1@Z) referenced in function void __cdecl RDKit::MolHash::generateMoleculeHashSet(class RDKit::ROMol const ,struct RDKit::MolHash::HashSet ,class std::vectorunsigned int,class std::allocatorunsigned int const *,class std::vectorunsigned int,class std::allocatorunsigned int const *) (?generateMoleculeHashSet@MolHash@RDKit@@YAXAEBVROMol@2@AEAUHashSet@12@PEBV?$vector@IV?$allocator@I@std@@@std@@2@Z) C:\RDKit\build\Code\GraphMol\MolHash\Wrap\MolHash.lib(MolHash.obj) rdMolHash Error 2 error LNK1120: 1 unresolved externals C:\RDKit\build\rdkit\Chem\Release\rdMolHash.pyd rdMolHash So I guess it would still be good to understand the threading issue (or at least for someone else to be able to reproduce it); and perhaps the observed MolHash issue is an easier one to sort(?) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.commailto:postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 tel:%2B44%20%280
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Hi James Thanks for your patience here. I will invest the time in trying to get automated builds happening on this Windows side so that this stops happening. I just pushed some changes that should clear up the MolHash-related build problems. I had forgotten that that bit of code still needed to be tested on Windows. I haven't tested building the cartridge on Windows (I'm not set up to do that), but the python wrappers definitely do build for me now with both RDK_BUILD_THREADSAFE_SSS and RDK_TEST_MULTITHREADED set to ON. I don't think it should make a difference, but just in case: I am doing this using boost 1.56. Best, -greg On Mon, Apr 13, 2015 at 11:30 AM, James Davidson j.david...@vernalis.com wrote: Here’s an update: Tried building rev5211, but saw similar linking errors (to do with Boost threading libraries). The most recent build that I have successfully managed without the errors is rev5016. It occurred to me that a couple of my cmake options relate to threading (RDK_BUILD_THREADSAFE=ON; RDK_TEST_MULTITHREADED=ON) – and perhaps other people (Greg, Paolo) with successful Windows builds had these set OFF (default)(?). Indeed, if I set both of these to OFF, I can successfully build rev5211, and all of the tests pass. So this is good – but I still don’t understand what has changed (in relation to Boost threading) that means that later versions don’t build… Threading aside, I was now feeling pretty confident that I would be ok to build the latest revision (rev5611). Unfortunately this was not the case – I initially hit a problem with MolHash.cpp, which I thought was down to MSVC being stupid about snprintf() (line 265). After a little stack-overflowing, I thought changing this to _snprintf() would solve the problem – which it appears to (at least MolHash.cpp now compiles), but then I get a couple of further errors down-stream (probably related to the change I made?): Error 1 error LNK2019: unresolved external symbol class std::basic_stringchar,struct std::char_traitschar,class std::allocatorchar __cdecl RDKit::Descriptors::calcMolFormula(class RDKit::ROMol const ,bool,bool) (?calcMolFormula@Descriptors@RDKit@ @YA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@ @AEBVROMol@2@_N1@Z) referenced in function void __cdecl RDKit::MolHash::generateMoleculeHashSet(class RDKit::ROMol const ,struct RDKit::MolHash::HashSet ,class std::vectorunsigned int,class std::allocatorunsigned int const *,class std::vectorunsigned int,class std::allocatorunsigned int const *) (?generateMoleculeHashSet@MolHash @RDKit@@YAXAEBVROMol@2@AEAUHashSet@12@PEBV?$vector@IV?$allocator@I@std@ @@std@@2@Z) C:\RDKit\build\Code\GraphMol\MolHash\Wrap\MolHash.lib(MolHash.obj) rdMolHash Error 2 error LNK1120: 1 unresolved externals C:\RDKit\build\rdkit\Chem\Release\rdMolHash.pyd rdMolHash So I guess it would still be good to understand the threading issue (or at least for someone else to be able to reproduce it); and perhaps the observed MolHash issue is an easier one to sort(?) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Here's an update: Tried building rev5211, but saw similar linking errors (to do with Boost threading libraries). The most recent build that I have successfully managed without the errors is rev5016. It occurred to me that a couple of my cmake options relate to threading (RDK_BUILD_THREADSAFE=ON; RDK_TEST_MULTITHREADED=ON) - and perhaps other people (Greg, Paolo) with successful Windows builds had these set OFF (default)(?). Indeed, if I set both of these to OFF, I can successfully build rev5211, and all of the tests pass. So this is good - but I still don't understand what has changed (in relation to Boost threading) that means that later versions don't build... Threading aside, I was now feeling pretty confident that I would be ok to build the latest revision (rev5611). Unfortunately this was not the case - I initially hit a problem with MolHash.cpp, which I thought was down to MSVC being stupid about snprintf() (line 265). After a little stack-overflowing, I thought changing this to _snprintf() would solve the problem - which it appears to (at least MolHash.cpp now compiles), but then I get a couple of further errors down-stream (probably related to the change I made?): Error 1 error LNK2019: unresolved external symbol class std::basic_stringchar,struct std::char_traitschar,class std::allocatorchar __cdecl RDKit::Descriptors::calcMolFormula(class RDKit::ROMol const ,bool,bool) (?calcMolFormula@Descriptors@RDKit@@YA?AV?$basic_string@DU?$char_traits@D@std@@V?$allocator@D@2@@std@@AEBVROMol@2@_N1@Z) referenced in function void __cdecl RDKit::MolHash::generateMoleculeHashSet(class RDKit::ROMol const ,struct RDKit::MolHash::HashSet ,class std::vectorunsigned int,class std::allocatorunsigned int const *,class std::vectorunsigned int,class std::allocatorunsigned int const *) (?generateMoleculeHashSet@MolHash@RDKit@@YAXAEBVROMol@2@AEAUHashSet@12@PEBV?$vector@IV?$allocator@I@std@@@std@@2@Z) C:\RDKit\build\Code\GraphMol\MolHash\Wrap\MolHash.lib(MolHash.obj) rdMolHash Error 2 error LNK1120: 1 unresolved externals C:\RDKit\build\rdkit\Chem\Release\rdMolHash.pyd rdMolHash So I guess it would still be good to understand the threading issue (or at least for someone else to be able to reproduce it); and perhaps the observed MolHash issue is an easier one to sort(?) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __-- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Hi Greg, James: one odd thing I notice about the error messages you posted is that they are all referencing a boost library that seems to be present in your build directory: Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA @XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost _thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Is this just MSVC being odd about how it reports errors or is there really a version of the boost threading library in your build\Code\GraphMol\DistGeomHelpers\Wrap directory? No boost threading library there... And I clear-out the build folder between builds anyway. So I guess it is a quirk of the reporting. I will have another go at building the latest version and report back on success or otherwise(!) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Here's an update: Using the version that's now in master (which has Paolo's pull request applied, thanks Paolo!), I was able to build and test the RDKit without unexpected problems on my windows box. James: one odd thing I notice about the error messages you posted is that they are all referencing a boost library that seems to be present in your build directory: Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_ thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Is this just MSVC being odd about how it reports errors or is there really a version of the boost threading library in your build\Code\GraphMol\DistGeomHelpers\Wrap directory? Best, -greg On Wed, Apr 8, 2015 at 5:59 PM, James Davidson j.david...@vernalis.com wrote: Hi Paolo, Unfortunately I have the impression that James' problem is related to neither of those. Might it be a boost/libboost naming issue? Perhaps, but cmake seems happy (see below)... James, could it be that you have multiple version of boost on your Windows machine and CMake is not picking the correct one? You might try to explicitly define on the CMake command line both BOOST_ROOT and BOOST_LIBRARYDIR location as I do on my system: C:\Program Files (x86)\CMake\bin\cmake -DBOOST_LIBRARYDIR=c:\32\boost_1_55_0_py34\lib32-msvc-12.0 -DBOOST_ROOT=c:\32\boost_1_55_0_py34 .. I do have multiple versions around, but I have the following set (from the cmake GUI): BOOST_LIBRARYDIRC:/local/boost_1_55_0-msvc-11.0-64/lib64-msvc-11.0 BOOST_ROOT C:/local/boost_1_55_0-msvc-11.0-64 and cmake reports that this version of boost is found: Boost version: 1.55.0 Found the following Boost libraries: regex So I am not sure what change is giving me the issue... Let's wait and see what Greg finds as well(!) -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Hi James, Greg, I just submitted a pull request which fixes: - one actual build failure on Windows (missing library dependency in Code/GraphMol/CMakeLists.txt) - one test failure on Windows (this was a CR+LF fix included in a previous pull request of mine which seems not to have been merged with trunk) Unfortunately I have the impression that James' problem is related to neither of those. Might it be a boost/libboost naming issue? Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom James, could it be that you have multiple version of boost on your Windows machine and CMake is not picking the correct one? You might try to explicitly define on the CMake command line both BOOST_ROOT and BOOST_LIBRARYDIR location as I do on my system: C:\Program Files (x86)\CMake\bin\cmake -DBOOST_LIBRARYDIR=c:\32\boost_1_55_0_py34\lib32-msvc-12.0 -DBOOST_ROOT=c:\32\boost_1_55_0_py34 .. Just a guess, though: that wouldn't explain why the RDKit builds pulling older revisions. Cheers, p. On 04/08/15 15:49, James Davidson wrote: Hi Greg – thanks! One extra piece: as of a few minutes ago, I can confirm that revision 4947 (last revision in Feb) builds, and passes all of the tests. Kind regards James *From:*Greg Landrum [mailto:greg.land...@gmail.com] *Sent:* 08 April 2015 15:14 *To:* James Davidson *Cc:* rdkit-discuss@lists.sourceforge.net *Subject:* Re: [Rdkit-discuss] Problem building recent revisions on Windows I will fire up windows tomorrow morning and ensure that things can build. It's been a couple weeks since I last did that. -greg On Wed, Apr 8, 2015 at 3:43 PM, James Davidson j.david...@vernalis.com mailto:j.david...@vernalis.com wrote: Dear All, I just tried building the latest RDKit build (rev. 5204) from the github repository, and hit a lot of link errors… So (somewhat at random) I tried an older build (5042), and saw very similar things (errors for this attempt are below). I am running on 64-bit Windows, and use cmake and Visual Studio 2012 – my build process hasn’t changed since the last time I successfully built (rev. 4274 – and I can confirm that if I roll-back to this revision, the build is once again successful), so I wondered if anyone more skilled in the art than me could suggest what the problem might be from the errors below(?) These are the errors when building the ‘ALL_BUILD’ project: Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2652 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2653 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2654 error LNK2005: public: class boost::thread::id __cdecl boost::thread::get_id(void)const (?get_id@thread@boost@@QEBA?AVid@12@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2656 error LNK2005: private: bool __cdecl boost::thread::join_noexcept(void) (?join_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2658 error LNK2005: public: bool __cdecl boost::thread::joinable(void)const (?joinable@thread@boost@@QEBA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2659 error LNK2005: private: bool __cdecl boost::thread::start_thread_noexcept(void) (?start_thread_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Hi Paolo, Unfortunately I have the impression that James' problem is related to neither of those. Might it be a boost/libboost naming issue? Perhaps, but cmake seems happy (see below)... James, could it be that you have multiple version of boost on your Windows machine and CMake is not picking the correct one? You might try to explicitly define on the CMake command line both BOOST_ROOT and BOOST_LIBRARYDIR location as I do on my system: C:\Program Files (x86)\CMake\bin\cmake -DBOOST_LIBRARYDIR=c:\32\boost_1_55_0_py34\lib32-msvc-12.0 -DBOOST_ROOT=c:\32\boost_1_55_0_py34 .. I do have multiple versions around, but I have the following set (from the cmake GUI): BOOST_LIBRARYDIRC:/local/boost_1_55_0-msvc-11.0-64/lib64-msvc-11.0 BOOST_ROOT C:/local/boost_1_55_0-msvc-11.0-64 and cmake reports that this version of boost is found: Boost version: 1.55.0 Found the following Boost libraries: regex So I am not sure what change is giving me the issue... Let's wait and see what Greg finds as well(!) Kind regards James __ PLEASE READ: This email is confidential and may be privileged. It is intended for the named addressee(s) only and access to it by anyone else is unauthorised. If you are not an addressee, any disclosure or copying of the contents of this email or any action taken (or not taken) in reliance on it is unauthorised and may be unlawful. If you have received this email in error, please notify the sender or postmas...@vernalis.com. Email is not a secure method of communication and the Company cannot accept responsibility for the accuracy or completeness of this message or any attachment(s). Please check this email for virus infection for which the Company accepts no responsibility. If verification of this email is sought then please request a hard copy. Unless otherwise stated, any views or opinions presented are solely those of the author and do not represent those of the Company. The Vernalis Group of Companies 100 Berkshire Place Wharfedale Road Winnersh, Berkshire RG41 5RD, England Tel: +44 (0)118 938 To access trading company registration and address details, please go to the Vernalis website at www.vernalis.com and click on the Company address and registration details link at the bottom of the page.. __ -- BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT Develop your own process in accordance with the BPMN 2 standard Learn Process modeling best practices with Bonita BPM through live exercises http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_ source=Sourceforge_BPM_Camp_5_6_15utm_medium=emailutm_campaign=VA_SF ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Hi Greg, I see rdkit currently uses Travis CI, but have you considered also using a Windows specific CI server like appveyor http://www.appveyor.com/ in addition? It is free for open source projects, and may guard against problems such as that seen in this thread in future development. I think the setup is very similar to travis, with an appveyor.yml config file specifying the windows specific build process. I’m afraid I'm not at all familiar with Windows, let alone how to build rdkit on it, otherwise I would attempt to offer a pull request. Thanks, Rich -- Richard Lewis PhD Candidate Centre for Molecular Informatics University of Cambridge http://www.ch.cam.ac.uk/group/bender http://www.ch.cam.ac.uk/group/bender On 8 Apr 2015, at 15:13, Greg Landrum greg.land...@gmail.com wrote: I will fire up windows tomorrow morning and ensure that things can build. It's been a couple weeks since I last did that. -greg On Wed, Apr 8, 2015 at 3:43 PM, James Davidson j.david...@vernalis.com mailto:j.david...@vernalis.com wrote: Dear All, I just tried building the latest RDKit build (rev. 5204) from the github repository, and hit a lot of link errors… So (somewhat at random) I tried an older build (5042), and saw very similar things (errors for this attempt are below). I am running on 64-bit Windows, and use cmake and Visual Studio 2012 – my build process hasn’t changed since the last time I successfully built (rev. 4274 – and I can confirm that if I roll-back to this revision, the build is once again successful), so I wondered if anyone more skilled in the art than me could suggest what the problem might be from the errors below(?) These are the errors when building the ‘ALL_BUILD’ project: Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2652 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2653 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2654 error LNK2005: public: class boost::thread::id __cdecl boost::thread::get_id(void)const (?get_id@thread@boost@@QEBA?AVid@12@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2656 error LNK2005: private: bool __cdecl boost::thread::join_noexcept(void) (?join_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2658 error LNK2005: public: bool __cdecl boost::thread::joinable(void)const (?joinable@thread@boost@@QEBA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2659 error LNK2005: private: bool __cdecl boost::thread::start_thread_noexcept(void) (?start_thread_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2660 error LNK1169: one or more multiply defined symbols foundC:\RDKit\build\rdkit\Chem\Release\rdDistGeom.pyd rdDistGeom Error 2675 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2676 error LNK2005: public: void __cdecl boost::thread::detach(void)
[Rdkit-discuss] Problem building recent revisions on Windows
Dear All, I just tried building the latest RDKit build (rev. 5204) from the github repository, and hit a lot of link errors... So (somewhat at random) I tried an older build (5042), and saw very similar things (errors for this attempt are below). I am running on 64-bit Windows, and use cmake and Visual Studio 2012 - my build process hasn't changed since the last time I successfully built (rev. 4274 - and I can confirm that if I roll-back to this revision, the build is once again successful), so I wondered if anyone more skilled in the art than me could suggest what the problem might be from the errors below(?) These are the errors when building the 'ALL_BUILD' project: Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2652 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2653 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2654 error LNK2005: public: class boost::thread::id __cdecl boost::thread::get_id(void)const (?get_id@thread@boost@@QEBA?AVid@12@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2656 error LNK2005: private: bool __cdecl boost::thread::join_noexcept(void) (?join_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2658 error LNK2005: public: bool __cdecl boost::thread::joinable(void)const (?joinable@thread@boost@@QEBA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2659 error LNK2005: private: bool __cdecl boost::thread::start_thread_noexcept(void) (?start_thread_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2660 error LNK1169: one or more multiply defined symbols found C:\RDKit\build\rdkit\Chem\Release\rdDistGeom.pydrdDistGeom Error 2675 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2676 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2677 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2678 error LNK2005: public: class boost::thread::id __cdecl boost::thread::get_id(void)const (?get_id@thread@boost@@QEBA?AVid@12@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2679 error LNK2005: private: bool __cdecl boost::thread::join_noexcept(void) (?join_noexcept@thread@boost@@AEAA_NXZ) already defined in
Re: [Rdkit-discuss] Problem building recent revisions on Windows
I will fire up windows tomorrow morning and ensure that things can build. It's been a couple weeks since I last did that. -greg On Wed, Apr 8, 2015 at 3:43 PM, James Davidson j.david...@vernalis.com wrote: Dear All, I just tried building the latest RDKit build (rev. 5204) from the github repository, and hit a lot of link errors… So (somewhat at random) I tried an older build (5042), and saw very similar things (errors for this attempt are below). I am running on 64-bit Windows, and use cmake and Visual Studio 2012 – my build process hasn’t changed since the last time I successfully built (rev. 4274 – and I can confirm that if I roll-back to this revision, the build is once again successful), so I wondered if anyone more skilled in the art than me could suggest what the problem might be from the errors below(?) These are the errors when building the ‘ALL_BUILD’ project: Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2652 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2653 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@ @YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2654 error LNK2005: public: class boost::thread::id __cdecl boost::thread::get_id(void)const (?get_id@thread@boost@ @QEBA?AVid@12@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2656 error LNK2005: private: bool __cdecl boost::thread::join_noexcept(void) (?join_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2658 error LNK2005: public: bool __cdecl boost::thread::joinable(void)const (?joinable@thread@boost@@QEBA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2659 error LNK2005: private: bool __cdecl boost::thread::start_thread_noexcept(void) (?start_thread_noexcept@thread @boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2660 error LNK1169: one or more multiply defined symbols foundC:\RDKit\build\rdkit\Chem\Release\rdDistGeom.pyd rdDistGeom Error 2675 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2676 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2677 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@ @YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2678 error LNK2005: public: class boost::thread::id __cdecl boost::thread::get_id(void)const (?get_id@thread@boost@ @QEBA?AVid@12@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2679 error LNK2005: private: bool __cdecl boost::thread::join_noexcept(void) (?join_noexcept@thread@boost@@AEAA_NXZ) already
Re: [Rdkit-discuss] Problem building recent revisions on Windows
Hi Greg – thanks! One extra piece: as of a few minutes ago, I can confirm that revision 4947 (last revision in Feb) builds, and passes all of the tests. Kind regards James From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 08 April 2015 15:14 To: James Davidson Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Problem building recent revisions on Windows I will fire up windows tomorrow morning and ensure that things can build. It's been a couple weeks since I last did that. -greg On Wed, Apr 8, 2015 at 3:43 PM, James Davidson j.david...@vernalis.commailto:j.david...@vernalis.com wrote: Dear All, I just tried building the latest RDKit build (rev. 5204) from the github repository, and hit a lot of link errors… So (somewhat at random) I tried an older build (5042), and saw very similar things (errors for this attempt are below). I am running on 64-bit Windows, and use cmake and Visual Studio 2012 – my build process hasn’t changed since the last time I successfully built (rev. 4274 – and I can confirm that if I roll-back to this revision, the build is once again successful), so I wondered if anyone more skilled in the art than me could suggest what the problem might be from the errors below(?) These are the errors when building the ‘ALL_BUILD’ project: Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2652 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2653 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2654 error LNK2005: public: class boost::thread::id __cdecl boost::thread::get_id(void)const (?get_id@thread@boost@@QEBA?AVid@12@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2656 error LNK2005: private: bool __cdecl boost::thread::join_noexcept(void) (?join_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2658 error LNK2005: public: bool __cdecl boost::thread::joinable(void)const (?joinable@thread@boost@@QEBA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2659 error LNK2005: private: bool __cdecl boost::thread::start_thread_noexcept(void) (?start_thread_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2660 error LNK1169: one or more multiply defined symbols found C:\RDKit\build\rdkit\Chem\Release\rdDistGeom.pydrdDistGeom Error 2675 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2676 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2677 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@@YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers
Re: [Rdkit-discuss] Problem building recent revisions on Windows
That's the second pointer to appveyor on this topic. Time for me to investigate. It would be awesome to have this happen automatically like with the linux builds on Travis. -greg On Wednesday, April 8, 2015, Rich Lewis rl...@cam.ac.uk wrote: Hi Greg, I see rdkit currently uses Travis CI, but have you considered also using a Windows specific CI server like appveyor http://www.appveyor.com/ in addition? It is free for open source projects, and may guard against problems such as that seen in this thread in future development. I think the setup is very similar to travis, with an appveyor.yml config file specifying the windows specific build process. I’m afraid I'm not at all familiar with Windows, let alone how to build rdkit on it, otherwise I would attempt to offer a pull request. Thanks, Rich -- Richard Lewis PhD Candidate Centre for Molecular Informatics University of Cambridge http://www.ch.cam.ac.uk/group/bender On 8 Apr 2015, at 15:13, Greg Landrum greg.land...@gmail.com javascript:_e(%7B%7D,'cvml','greg.land...@gmail.com'); wrote: I will fire up windows tomorrow morning and ensure that things can build. It's been a couple weeks since I last did that. -greg On Wed, Apr 8, 2015 at 3:43 PM, James Davidson j.david...@vernalis.com javascript:_e(%7B%7D,'cvml','j.david...@vernalis.com'); wrote: Dear All, I just tried building the latest RDKit build (rev. 5204) from the github repository, and hit a lot of link errors… So (somewhat at random) I tried an older build (5042), and saw very similar things (errors for this attempt are below). I am running on 64-bit Windows, and use cmake and Visual Studio 2012 – my build process hasn’t changed since the last time I successfully built (rev. 4274 – and I can confirm that if I roll-back to this revision, the build is once again successful), so I wondered if anyone more skilled in the art than me could suggest what the problem might be from the errors below(?) These are the errors when building the ‘ALL_BUILD’ project: Error 2651 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2652 error LNK2005: public: void __cdecl boost::thread::detach(void) (?detach@thread@boost@@QEAAXXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2653 error LNK2005: class boost::thread::id __cdecl boost::this_thread::get_id(void) (?get_id@this_thread@boost@ @YA?AVid@thread@2@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2654 error LNK2005: public: class boost::thread::id __cdecl boost::thread::get_id(void)const (?get_id@thread@boost@ @QEBA?AVid@12@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2656 error LNK2005: private: bool __cdecl boost::thread::join_noexcept(void) (?join_noexcept@thread@boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2658 error LNK2005: public: bool __cdecl boost::thread::joinable(void)const (?joinable@thread@boost@@QEBA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2659 error LNK2005: private: bool __cdecl boost::thread::start_thread_noexcept(void) (?start_thread_noexcept@thread @boost@@AEAA_NXZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\DistGeomHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdDistGeom Error 2660 error LNK1169: one or more multiply defined symbols foundC:\RDKit\build\rdkit\Chem\Release\rdDistGeom.pyd rdDistGeom Error 2675 error LNK2005: public: virtual __cdecl boost::detail::thread_data_base::~thread_data_base(void) (??1thread_data_base@detail@boost@@UEAA@XZ) already defined in boost_thread-vc110-mt-1_55.lib(boost_thread-vc110-mt-1_55.dll) C:\RDKit\build\Code\GraphMol\ForceFieldHelpers\Wrap\libboost_thread-vc110-mt-1_55.lib(thread.obj) rdForceFieldHelpers Error 2676 error LNK2005: public:
