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Install Open Babel from Source Code on CentOS
How to download and instal Open Babel from source code on CentOS computers? I want to build the binary programs by myself.
✍: FYIcenter.com
If you want to build the Open Babel binary programs from source code yourself,
you can follow this tutorial.
1. Go to Open Babel Code Repository at https://sourceforge.net/projects/openbabel/.
2. Open "Files > openbabel / 2.4.1" folder. And download openbabel-2.4.1.tar.gz.
3. Unzip and untar the download file. You should see a directory ~/openbabel-2.4.1 with all source code.
4. Create a "build" sub-directory and configure the build system.
fyicenter$ cd openbabel-2.4.1/ fyicenter$ mkdir build fyicenter$ cd build fyicenter$ cmake .. -- The C compiler identification is GNU 8.3.1 -- The CXX compiler identification is GNU 8.3.1 ... -- Checking for module 'cairo' -- Package 'cairo', required by 'virtual:world', not found -- Could NOT find Cairo (missing: CAIRO_LIBRARIES CAIRO_INCLUDE_DIRS) -- Could NOT find Cairo. PNG output will NOT be supported. -- Looking for getopt -- Looking for getopt - found -- Attempting to build the GUI -- wxWidgets not found => GUI will not be built -- Found PythonInterp: /usr/bin/python3.6 (found version "3.6.8") -- Configuring done -- Generating done -- Build files have been written to: /home/fyicenter/openbabel-2.4.1/build
5. Run the build process.
fyicenter$ make -j2 Scanning dependencies of target inchi Scanning dependencies of target openbabel [ 0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.o [ 0%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_bns.o [ 0%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichi_io.o [ 0%] Building C object src/formats/libinchi/CMakeFiles/inchi.dir/ichican2.o [ 1%] Building CXX object src/CMakeFiles/openbabel.dir/atom.o ... [ 99%] Building CXX object test/CMakeFiles/test_runner.dir/smartstest.o [ 99%] Building CXX object test/CMakeFiles/test_runner.dir/smartsparse.o [ 99%] Building CXX object test/CMakeFiles/test_runner.dir/smilesmatch.o [100%] Building CXX object test/CMakeFiles/test_runner.dir/unitcell.o [100%] Building CXX object test/CMakeFiles/test_runner.dir/obtest.o [100%] Linking CXX executable ../bin/test_runner [100%] Built target test_runner
6. Run tests on the build result. You may see some failures.
fyicenter$ make test Running tests... Test project /home/fyicenter/openbabel-2.4.1/build Start 1: test_automorphism_1 1/151 Test #1: test_automorphism_1 .............. Passed 0.01 sec Start 2: test_automorphism_2 2/151 Test #2: test_automorphism_2 .............. Passed 0.01 sec Start 3: test_automorphism_3 3/151 Test #3: test_automorphism_3 .............. Passed 0.01 sec Start 4: test_automorphism_4 ... 150/151 Test #150: pytest_kekule .................... Passed 0.32 sec Start 151: pytest_pdbformat 151/151 Test #151: pytest_pdbformat .................***Failed 0.03 sec 94% tests passed, 9 tests failed out of 151 Total Test time (real) = 21.85 sec The following tests FAILED: 42 - test_gzip_1 (Failed) 53 - test_isomorphism_5 (Failed) 54 - test_isomorphism_6 (Failed) 57 - test_multicml_1 (Failed) 64 - test_rotor_2 (Failed) 65 - test_rotor_3 (Failed) 66 - test_rotor_4 (Failed) 146 - pytest_sym (Failed) 151 - pytest_pdbformat (Failed) Errors while running CTest make: *** [Makefile:73: test] Error 8
7. Build final installation targets and install them to the default system location.
fyicenter$ sudo make install [ 14%] Built target openbabel [ 16%] Built target plugin_descriptors [ 20%] Built target plugin_ops [ 21%] Built target plugin_fingerprints [ 22%] Built target plugin_forcefields ... [ 88%] Built target test_inchiwrite [100%] Built target test_runner [100%] Built target roundtrip Install the project... -- Install configuration: "RelWithDebInfo" -- Installing: /usr/local/include/openbabel-2.0/openbabel/babelconfig.h -- Installing: /usr/local/lib/pkgconfig/openbabel-2.0.pc -- Installing: /usr/local/lib/cmake/openbabel2/OpenBabel2_EXPORTS.cmake -- Installing: /usr/local/lib/cmake/openbabel2/OpenBabel2_EXPORTS-relwithdebinfo.cmake -- Installing: /usr/local/lib/cmake/openbabel2/OpenBabel2Config.cmake -- Installing: /usr/local/lib/cmake/openbabel2/OpenBabel2ConfigVersion.cmake -- Installing: /usr/local/include/inchi/inchi_api.h ... -- Installing: /usr/local/bin/obthermo -- Set runtime path of "/usr/local/bin/obthermo" to "/usr/local/lib" -- Installing: /usr/local/bin/obspectrophore -- Set runtime path of "/usr/local/bin/obspectrophore" to "/usr/local/lib" -- Installing: /usr/local/bin/obgrep -- Set runtime path of "/usr/local/bin/obgrep" to "/usr/local/lib" -- Installing: /usr/local/bin/roundtrip -- Set runtime path of "/usr/local/bin/roundtrip" to "/usr/local/lib"
7. Verify installation.
fyicenter$ babel -V Open Babel 2.4.1 -- May 25 2020 -- 08:24:13
Open Babel command line tools are ready to use.
Note that the building process requires you to have building tools: GCC compiler, CMake, and make.
You can also download Open Babel source code from github.com as https://github.com/openbabel/openbabel
⇐ Install Open Babel CLI RPM Package for CentOS
2020-10-10, 1547👍, 0💬
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