[Rdkit-discuss] Error compiling RDKit with MinGW on Windows
Hi everyone, I have been trying to compile RDKit (rdkit-Release_2016_03_2.tar.gz) using CodeBlocks 16.01 with the MinGW (gcc 4.9) compiler on Win7. But I keep getting the following error in the LocaleSwitcher.cpp: [] [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.obj cd /d D:\Programme\RDKit\rdkit_2\build\Code\RDGeneral && C:\PROGRA~2\CODEBL~1\MinGW\bin\G__~1.EXE -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION @CMakeFiles/RDGeneral.dir/includes_CXX.rsp -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles\RDGeneral.dir\Dict.cpp.obj -c D:\Programme\RDKit\rdkit_2\Code\RDGeneral\Dict.cpp D:\Programme\RDKit\rdkit_2\Code\RDGeneral\Dict.cpp:1:0: warning: -fPIC ignored for target (all code is position independent) // $Id$ ^ D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp:1:0: warning: -fPIC ignored for target (all code is position independent) // Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc. ^ D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp:36:21: fatal error: xlocale.h: No such file or directory #include ^ compilation terminated. mingw32-make.exe[2]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj] Error 1 mingw32-make.exe[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] Error 2 mingw32-make.exe: *** [all] Error 2 [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj cd /d D:\Programme\RDKit\rdkit_2\build\Code\RDGeneral && C:\PROGRA~2\CODEBL~1\MinGW\bin\G__~1.EXE -DRDGeneral_EXPORTS -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_USE_STRICT_ROTOR_DEFINITION @CMakeFiles/RDGeneral.dir/includes_CXX.rsp -mpopcnt -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 -DNDEBUG -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o CMakeFiles\RDGeneral.dir\LocaleSwitcher.cpp.obj -c D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp Code\RDGeneral\CMakeFiles\RDGeneral.dir\build.make:187: recipe for target 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj' failed mingw32-make.exe[2]: Leaving directory 'D:/Programme/RDKit/rdkit_2/build' CMakeFiles\Makefile2:279: recipe for target 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/all' failed mingw32-make.exe[1]: Leaving directory 'D:/Programme/RDKit/rdkit_2/build' D:/Programme/RDKit/rdkit_2/build/Makefile:159: recipe for target 'all' failed Process terminated with status 2 (0 minute(s), 17 second(s)) 4 error(s), 6 warning(s) (0 minute(s), 17 second(s)) Since the error says that xlocale.h is missing, I downloaded and tried do add that header-file to the mingw include directory but this just lead to different (missing file) errors. So there seems to be a more general problem . I'm not sure if it occurs due to a linking error or if I'm doing something else wrong. Since I am quite new to programming it might be something obvious which I am not aware of. To get the build recipe I used Cmake. The configuration and generation of the CodeBlocks-project file worked fine. I also compiled the boost library that way using the same compiler and it seems to work, too. Any ideas about what I am doing wrong would be greatly appreciated. Best Regards, Anne -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.
Dear all, I just tried to build the current Release_2016_03_2 with conda on Ubuntu 16.04 and ran into an error. I used a fresh clone of conda-rdkit and changed the git tag in rdkit/meta.yaml from Release_2016_03_1 to Release_2016_03_2. Then: $ conda build boost This ran without problems. Then: $ conda build rdkit This gave the traceback shown below, which left me at a loss. Does anyone have any ideas? Many thanks in advance. Kind regards, Axel Traceback: [...] checkout: 'Release_2016_03_2' Cloning into '/home/pahl/anaconda3/conda-bld/work'... done. Note: checking out 'Release_2016_03_2'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at e0c1c02... update release notes ==> git log -n1 <== commit e0c1c0296a0632089ec02550a006d2e9bd0fec96 Author: Greg Landrum Date: Fri May 20 14:52:46 2016 +0200 update release notes ==> git describe --tags --dirty <== Release_2016_03_2 ==> git status <== HEAD detached at Release_2016_03_2 nothing to commit, working directory clean Applying patch: '/home/pahl/dev/github/conda-rdkit/rdkit/rdpaths.patch' Patch level ambiguous, selecting least deep patching file rdkit/CMakeLists.txt Applying patch: '/home/pahl/dev/github/conda-rdkit/rdkit/rddepictor.patch' patching file Code/GraphMol/Depictor/RDDepictor.cpp Hunk #1 FAILED at 133. 1 out of 1 hunk FAILED -- saving rejects to file Code/GraphMol/Depictor/RDDepictor.cpp.rej Warning: failed to download source. If building, will try again after downloading recipe dependencies. Error was: Command '['/usr/bin/patch', '-p0', '-i', '/home/pahl/dev/github/conda-rdkit/rdkit/rddepictor.patch']' returned non-zero exit status 1 An unexpected error has occurred, please consider sending the following traceback to the conda GitHub issue tracker at: https://github.com/conda/conda-build/issues Include the output of the command 'conda info' in your report. Traceback (most recent call last): File "/home/pahl/anaconda3/bin/conda-build", line 5, in sys.exit(main()) File "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py", line 140, in main args_func(args, p) File "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py", line 380, in args_func args.func(args, p) File "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py", line 327, in execute dirty=args.dirty) File "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/build.py", line 487, in build assert not need_source_download, "Source download failed. Please investigate." AssertionError: Source download failed. Please investigate. -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Error compiling RDKit with MinGW on Windows
On 23/06/16 13:29, Anne wrote: > Hi everyone, > > I have been trying to compile RDKit (rdkit-Release_2016_03_2.tar.gz) > using CodeBlocks 16.01 with the MinGW (gcc 4.9) compiler on Win7. But I > keep getting the following error in the LocaleSwitcher.cpp: > > [] > > [ 1%] Building CXX object > Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.obj > cd /d D:\Programme\RDKit\rdkit_2\build\Code\RDGeneral && > C:\PROGRA~2\CODEBL~1\MinGW\bin\G__~1.EXE -DRDGeneral_EXPORTS > -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED > -DRDK_USE_STRICT_ROTOR_DEFINITION > @CMakeFiles/RDGeneral.dir/includes_CXX.rsp -mpopcnt -Wno-deprecated > -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 > -DNDEBUG -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o > CMakeFiles\RDGeneral.dir\Dict.cpp.obj -c > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\Dict.cpp > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\Dict.cpp:1:0: warning: -fPIC > ignored for target (all code is position independent) >// $Id$ >^ > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp:1:0: > warning: -fPIC ignored for target (all code is position independent) >// Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc. >^ > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp:36:21: > fatal error: xlocale.h: No such file or directory >#include >^ > compilation terminated. > mingw32-make.exe[2]: *** > [Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj] Error 1 > mingw32-make.exe[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] > Error 2 > mingw32-make.exe: *** [all] Error 2 > [ 1%] Building CXX object > Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj > cd /d D:\Programme\RDKit\rdkit_2\build\Code\RDGeneral && > C:\PROGRA~2\CODEBL~1\MinGW\bin\G__~1.EXE -DRDGeneral_EXPORTS > -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED > -DRDK_USE_STRICT_ROTOR_DEFINITION > @CMakeFiles/RDGeneral.dir/includes_CXX.rsp -mpopcnt -Wno-deprecated > -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 > -DNDEBUG -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o > CMakeFiles\RDGeneral.dir\LocaleSwitcher.cpp.obj -c > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp > Code\RDGeneral\CMakeFiles\RDGeneral.dir\build.make:187: recipe for > target 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj' > failed > mingw32-make.exe[2]: Leaving directory 'D:/Programme/RDKit/rdkit_2/build' > CMakeFiles\Makefile2:279: recipe for target > 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/all' failed > mingw32-make.exe[1]: Leaving directory 'D:/Programme/RDKit/rdkit_2/build' > D:/Programme/RDKit/rdkit_2/build/Makefile:159: recipe for target 'all' > failed > Process terminated with status 2 (0 minute(s), 17 second(s)) > 4 error(s), 6 warning(s) (0 minute(s), 17 second(s)) > > > Since the error says that xlocale.h is missing, I downloaded and tried > do add that header-file to the mingw include directory but this just > lead to different (missing file) errors. So there seems to be a more > general problem . I'm not sure if it occurs due to a linking error or if > I'm doing something else wrong. Since I am quite new to programming it > might be something obvious which I am not aware of. > > To get the build recipe I used Cmake. The configuration and generation > of the CodeBlocks-project file worked fine. I also compiled the boost > library that way using the same compiler and it seems to work, too. > > This is a compilation error (not a linking error). The functions that you might need in LocaleSwitcher.cpp might be available in locale.h. So you might try changing to Or maybe provides what you need so that you can comment out that line completely: // #include (These are just guesses.) Paul. -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Error compiling RDKit with MinGW on Windows
Dear Anne, tonight I'll be working on getting a working RDKit build using MinGW compilers; I'll update you as soon as I have finished. Best, Paolo On 23/06/2016 13:29, Anne wrote: > Hi everyone, > > I have been trying to compile RDKit (rdkit-Release_2016_03_2.tar.gz) > using CodeBlocks 16.01 with the MinGW (gcc 4.9) compiler on Win7. But I > keep getting the following error in the LocaleSwitcher.cpp: > > [] > > [ 1%] Building CXX object > Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.obj > cd /d D:\Programme\RDKit\rdkit_2\build\Code\RDGeneral && > C:\PROGRA~2\CODEBL~1\MinGW\bin\G__~1.EXE -DRDGeneral_EXPORTS > -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED > -DRDK_USE_STRICT_ROTOR_DEFINITION > @CMakeFiles/RDGeneral.dir/includes_CXX.rsp -mpopcnt -Wno-deprecated > -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 > -DNDEBUG -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o > CMakeFiles\RDGeneral.dir\Dict.cpp.obj -c > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\Dict.cpp > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\Dict.cpp:1:0: warning: -fPIC > ignored for target (all code is position independent) >// $Id$ >^ > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp:1:0: > warning: -fPIC ignored for target (all code is position independent) >// Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc. >^ > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp:36:21: > fatal error: xlocale.h: No such file or directory >#include >^ > compilation terminated. > mingw32-make.exe[2]: *** > [Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj] Error 1 > mingw32-make.exe[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] > Error 2 > mingw32-make.exe: *** [all] Error 2 > [ 1%] Building CXX object > Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj > cd /d D:\Programme\RDKit\rdkit_2\build\Code\RDGeneral && > C:\PROGRA~2\CODEBL~1\MinGW\bin\G__~1.EXE -DRDGeneral_EXPORTS > -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED > -DRDK_USE_STRICT_ROTOR_DEFINITION > @CMakeFiles/RDGeneral.dir/includes_CXX.rsp -mpopcnt -Wno-deprecated > -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 > -DNDEBUG -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o > CMakeFiles\RDGeneral.dir\LocaleSwitcher.cpp.obj -c > D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp > Code\RDGeneral\CMakeFiles\RDGeneral.dir\build.make:187: recipe for > target 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj' > failed > mingw32-make.exe[2]: Leaving directory 'D:/Programme/RDKit/rdkit_2/build' > CMakeFiles\Makefile2:279: recipe for target > 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/all' failed > mingw32-make.exe[1]: Leaving directory 'D:/Programme/RDKit/rdkit_2/build' > D:/Programme/RDKit/rdkit_2/build/Makefile:159: recipe for target 'all' > failed > Process terminated with status 2 (0 minute(s), 17 second(s)) > 4 error(s), 6 warning(s) (0 minute(s), 17 second(s)) > > > Since the error says that xlocale.h is missing, I downloaded and tried > do add that header-file to the mingw include directory but this just > lead to different (missing file) errors. So there seems to be a more > general problem . I'm not sure if it occurs due to a linking error or if > I'm doing something else wrong. Since I am quite new to programming it > might be something obvious which I am not aware of. > > To get the build recipe I used Cmake. The configuration and generation > of the CodeBlocks-project file worked fine. I also compiled the boost > library that way using the same compiler and it seems to work, too. > > Any ideas about what I am doing wrong would be greatly appreciated. > > > Best Regards, > > Anne > > > -- > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Error compiling RDKit with MinGW on Windows
Mingw apparently doesn't support xlocale. There are a few issues floating around when doing a brief web search. One option is to simply revert back to the older code for mingw, however we also may need to disable the regression test in this case. I can supply a patch for this once I get mingw installed. Brian Kelley > On Jun 23, 2016, at 1:47 PM, Paolo Tosco wrote: > > Dear Anne, > > tonight I'll be working on getting a working RDKit build using MinGW > compilers; I'll update you as soon as I have finished. > > Best, > Paolo > >> On 23/06/2016 13:29, Anne wrote: >> Hi everyone, >> >> I have been trying to compile RDKit (rdkit-Release_2016_03_2.tar.gz) >> using CodeBlocks 16.01 with the MinGW (gcc 4.9) compiler on Win7. But I >> keep getting the following error in the LocaleSwitcher.cpp: >> >> [] >> >> [ 1%] Building CXX object >> Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.obj >> cd /d D:\Programme\RDKit\rdkit_2\build\Code\RDGeneral && >> C:\PROGRA~2\CODEBL~1\MinGW\bin\G__~1.EXE -DRDGeneral_EXPORTS >> -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED >> -DRDK_USE_STRICT_ROTOR_DEFINITION >> @CMakeFiles/RDGeneral.dir/includes_CXX.rsp -mpopcnt -Wno-deprecated >> -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 >> -DNDEBUG -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o >> CMakeFiles\RDGeneral.dir\Dict.cpp.obj -c >> D:\Programme\RDKit\rdkit_2\Code\RDGeneral\Dict.cpp >> D:\Programme\RDKit\rdkit_2\Code\RDGeneral\Dict.cpp:1:0: warning: -fPIC >> ignored for target (all code is position independent) >> // $Id$ >> ^ >> D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp:1:0: >> warning: -fPIC ignored for target (all code is position independent) >> // Copyright (c) 2016, Novartis Institutes for BioMedical Research Inc. >> ^ >> D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp:36:21: >> fatal error: xlocale.h: No such file or directory >> #include >> ^ >> compilation terminated. >> mingw32-make.exe[2]: *** >> [Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj] Error 1 >> mingw32-make.exe[1]: *** [Code/RDGeneral/CMakeFiles/RDGeneral.dir/all] >> Error 2 >> mingw32-make.exe: *** [all] Error 2 >> [ 1%] Building CXX object >> Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj >> cd /d D:\Programme\RDKit\rdkit_2\build\Code\RDGeneral && >> C:\PROGRA~2\CODEBL~1\MinGW\bin\G__~1.EXE -DRDGeneral_EXPORTS >> -DRDK_32BIT_BUILD -DRDK_TEST_MULTITHREADED >> -DRDK_USE_STRICT_ROTOR_DEFINITION >> @CMakeFiles/RDGeneral.dir/includes_CXX.rsp -mpopcnt -Wno-deprecated >> -Wno-unused-function -fno-strict-aliasing -fPIC -Wall -Wextra -O3 >> -DNDEBUG -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB -o >> CMakeFiles\RDGeneral.dir\LocaleSwitcher.cpp.obj -c >> D:\Programme\RDKit\rdkit_2\Code\RDGeneral\LocaleSwitcher.cpp >> Code\RDGeneral\CMakeFiles\RDGeneral.dir\build.make:187: recipe for >> target 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.obj' >> failed >> mingw32-make.exe[2]: Leaving directory 'D:/Programme/RDKit/rdkit_2/build' >> CMakeFiles\Makefile2:279: recipe for target >> 'Code/RDGeneral/CMakeFiles/RDGeneral.dir/all' failed >> mingw32-make.exe[1]: Leaving directory 'D:/Programme/RDKit/rdkit_2/build' >> D:/Programme/RDKit/rdkit_2/build/Makefile:159: recipe for target 'all' >> failed >> Process terminated with status 2 (0 minute(s), 17 second(s)) >> 4 error(s), 6 warning(s) (0 minute(s), 17 second(s)) >> >> >> Since the error says that xlocale.h is missing, I downloaded and tried >> do add that header-file to the mingw include directory but this just >> lead to different (missing file) errors. So there seems to be a more >> general problem . I'm not sure if it occurs due to a linking error or if >> I'm doing something else wrong. Since I am quite new to programming it >> might be something obvious which I am not aware of. >> >> To get the build recipe I used Cmake. The configuration and generation >> of the CodeBlocks-project file worked fine. I also compiled the boost >> library that way using the same compiler and it seems to work, too. >> >> Any ideas about what I am doing wrong would be greatly appreciated. >> >> >> Best Regards, >> >> Anne >> >> >> -- >> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San >> Francisco, CA to explore cutting-edge tech and listen to tech luminaries >> present their vision of the future. This family event has something for >> everyone, including kids. Get more information and register today. >> http://sdm.link/attshape >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > -- > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA
Re: [Rdkit-discuss] Struggling with apache + rdkit + django
Le 22/06/2016 à 02:56, Stéphane Téletchéa a écrit : > Since I have tried to reproduce all the > steps properly I'll set up soon a post > on my blog about this, so others will be able to reproduce easily the > initial steps without being blocked like > me for some days ... Once the post is up, I'll post it here. Dear all, I tool little time to assemble my tests on a dedicated page, with no github link for now, but most (if not all) code is indicated in the blog post. Thanks again for the comments and remarks, I hope this entry will be useful to someone else than me :-) http://www.steletch.org/spip.php?article91 Many thanks, Stéphane -- Lecturer, UFIP, UMR 6286 CNRS, Team Protein Design In Silico UFR Sciences et Techniques, 2, rue de la Houssinière, Bât. 25, 44322 Nantes cedex 03, France Tél : +33 251 125 636 / Fax : +33 251 125 632 http://www.ufip.univ-nantes.fr/ - http://www.steletch.org -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] conda build of Release_2016_03_2 failed on Ubuntu 16.04.
Hi Axel, Apologies that I forgot to update the conda-rdkit repo when I did the patch release. I just fixed the conda build recipe so that it uses 2016_03_2. One note: when I built on ubuntu 16.04 I also needed to rebuild a local copy of boost. You can do this by just doing a "conda build boost" before "conda build rdkit" Best, -greg On Thu, Jun 23, 2016 at 6:06 PM, Axel Pahl wrote: > Dear all, > > I just tried to build the current Release_2016_03_2 with conda on Ubuntu > 16.04 and ran into an error. > > I used a fresh clone of conda-rdkit and changed the git tag in > rdkit/meta.yaml from Release_2016_03_1 to Release_2016_03_2. > Then: > > $ conda build boost > This ran without problems. Then: > > $ conda build rdkit > This gave the traceback shown below, which left me at a loss. > Does anyone have any ideas? > Many thanks in advance. > > Kind regards, > Axel > > Traceback: > [...] > checkout: 'Release_2016_03_2' > Cloning into '/home/pahl/anaconda3/conda-bld/work'... > done. > Note: checking out 'Release_2016_03_2'. > > You are in 'detached HEAD' state. You can look around, make experimental > changes and commit them, and you can discard any commits you make in this > state without impacting any branches by performing another checkout. > > If you want to create a new branch to retain commits you create, you may > do so (now or later) by using -b with the checkout command again. Example: > >git checkout -b > > HEAD is now at e0c1c02... update release notes > ==> git log -n1 <== > > commit e0c1c0296a0632089ec02550a006d2e9bd0fec96 > Author: Greg Landrum > Date: Fri May 20 14:52:46 2016 +0200 > > update release notes > > > ==> git describe --tags --dirty <== > > Release_2016_03_2 > > > ==> git status <== > > HEAD detached at Release_2016_03_2 > nothing to commit, working directory clean > > > Applying patch: '/home/pahl/dev/github/conda-rdkit/rdkit/rdpaths.patch' > Patch level ambiguous, selecting least deep > patching file rdkit/CMakeLists.txt > Applying patch: '/home/pahl/dev/github/conda-rdkit/rdkit/rddepictor.patch' > patching file Code/GraphMol/Depictor/RDDepictor.cpp > Hunk #1 FAILED at 133. > 1 out of 1 hunk FAILED -- saving rejects to file > Code/GraphMol/Depictor/RDDepictor.cpp.rej > Warning: failed to download source. If building, will try again after > downloading recipe dependencies. > Error was: > Command '['/usr/bin/patch', '-p0', '-i', > '/home/pahl/dev/github/conda-rdkit/rdkit/rddepictor.patch']' returned > non-zero exit status 1 > An unexpected error has occurred, please consider sending the > following traceback to the conda GitHub issue tracker at: > > https://github.com/conda/conda-build/issues > > Include the output of the command 'conda info' in your report. > > > Traceback (most recent call last): >File "/home/pahl/anaconda3/bin/conda-build", line 5, in > sys.exit(main()) >File > > "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py", > line 140, in main > args_func(args, p) >File > > "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py", > line 380, in args_func > args.func(args, p) >File > > "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/main_build.py", > line 327, in execute > dirty=args.dirty) >File > "/home/pahl/anaconda3/lib/python3.5/site-packages/conda_build/build.py", > line 487, in build > assert not need_source_download, "Source download failed. Please > investigate." > AssertionError: Source download failed. Please investigate. > > > -- > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San Francisco, CA to explore cutting-edge tech and listen to tech luminaries present their vision of the future. This family event has something for everyone, including kids. Get more information and register today. http://sdm.link/attshape___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
