fredrikw
commented
6 years ago According to the log, it can't find MySQL. Make sure that you have the development package of MySQL installed, usually called something like mysql_dev.
Closed AspirinCode closed 6 years ago
fredrikw
commented
6 years ago According to the log, it can't find MySQL. Make sure that you have the development package of MySQL installed, usually called something like mysql_dev.
AspirinCode
commented
6 years ago [root@aspirin build]# make Scanning dependencies of target mychem-lib [ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o In file included from /home/Aspirin/Downloads/mychem-0.9.3/src/conversion.h:45:0, from /home/Aspirin/Downloads/mychem-0.9.3/src/conversion.c:31: /usr/local/mysql/include/my_global.h:362:6: warning: "_WIN32" is not defined [-Wundef]
^/usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
^[ 7%] Building CXX object src/CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o
In file included from /home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:40:0:
/home/Aspirin/Downloads/mychem-0.9.3/src/fingerprints/finger2.cpp:48:21: warning: unused parameter ‘fp’ [-Wunused-parameter]
virtual std::string DescribeBits(const std:: vector
^/usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
^[ 14%] Building CXX object src/CMakeFiles/mychem-lib.dir/helper_wrapper.cpp.o [ 18%] Building C object src/CMakeFiles/mychem-lib.dir/modification.c.o In file included from /home/Aspirin/Downloads/mychem-0.9.3/src/modification.h:45:0, from /home/Aspirin/Downloads/mychem-0.9.3/src/modification.c:31: /usr/local/mysql/include/my_global.h:362:6: warning: "_WIN32" is not defined [-Wundef]
^/usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
^[ 22%] Building CXX object src/CMakeFiles/mychem-lib.dir/modification_wrapper.cpp.o [ 25%] Building C object src/CMakeFiles/mychem-lib.dir/molmatch.c.o In file included from /home/Aspirin/Downloads/mychem-0.9.3/src/molmatch.h:45:0, from /home/Aspirin/Downloads/mychem-0.9.3/src/molmatch.c:31: /usr/local/mysql/include/my_global.h:362:6: warning: "_WIN32" is not defined [-Wundef]
^/usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
^[ 29%] Building CXX object src/CMakeFiles/mychem-lib.dir/molmatch_wrapper.cpp.o [ 33%] Building C object src/CMakeFiles/mychem-lib.dir/property.c.o In file included from /home/Aspirin/Downloads/mychem-0.9.3/src/property.h:47:0, from /home/Aspirin/Downloads/mychem-0.9.3/src/property.c:33: /usr/local/mysql/include/my_global.h:362:6: warning: "_WIN32" is not defined [-Wundef]
^/usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
^[ 37%] Building CXX object src/CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o
In file included from /home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:41:0:
/home/Aspirin/Downloads/mychem-0.9.3/src/descriptors/groupcontrib.cpp: In member function ‘virtual double OpenBabel::OBGroupContrib::Predict(OpenBabel::OBBase, std::string)’:
/home/Aspirin/Downloads/mychem-0.9.3/src/descriptors/groupcontrib.cpp:160:49: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int index = 0; index < tmpmol.NumAtoms(); index++) {
^
/home/Aspirin/Downloads/mychem-0.9.3/src/descriptors/groupcontrib.cpp: At global scope:
/home/Aspirin/Downloads/mychem-0.9.3/src/descriptors/groupcontrib.cpp:104:10: warning: unused parameter ‘param’ [-Wunused-parameter]
double OBGroupContrib::Predict(OBBase pOb, string param)
^
[ 40%] Building CXX object src/CMakeFiles/mychem-lib.dir/serialization.cpp.o
[ 44%] Building CXX object src/CMakeFiles/mychem-lib.dir/dlhandler_unix.cpp.o
Linking CXX shared library libmychem.so
CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o: In function conversion': /home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:71: undefined reference toOpenBabel::OBConversion::SetInAndOutFormats(char const, char const)'
CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o: In function conversionV3000': /home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:113: undefined reference toOpenBabel::OBConversion::SetInAndOutFormats(char const, char const)'
CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o: In function V3000conversion': /home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:156: undefined reference toOpenBabel::OBConversion::SetInAndOutFormats(char const, char const)'
CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o: In function CMLconversion': /home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:191: undefined reference toOpenBabel::OBConversion::SetInAndOutFormats(char const, char const)'
CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o: In function conversionCML': /home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:223: undefined reference toOpenBabel::OBConversion::SetInAndOutFormats(char const, char const)'
CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o:/home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:304: more undefined references to OpenBabel::OBConversion::SetInAndOutFormats(char const*, char const*)' follow CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o: In functionconversionFPT':
/home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:256: undefined reference to OpenBabel::OBConversion::SetInFormat(char const*)' CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o: In functionserializeMolecule':
/home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:335: undefined reference to OpenBabel::OBConversion::SetInFormat(char const*)' CMakeFiles/mychem-lib.dir/modification_wrapper.cpp.o: In functionob_add_hydrogens':
/home/Aspirin/Downloads/mychem-0.9.3/src/modification_wrapper.cpp:61: undefined reference to OpenBabel::OBConversion::SetInAndOutFormats(char const*, char const*)' CMakeFiles/mychem-lib.dir/modification_wrapper.cpp.o: In functionob_remove_hydrogens':
/home/Aspirin/Downloads/mychem-0.9.3/src/modification_wrapper.cpp:91: undefined reference to OpenBabel::OBConversion::SetInAndOutFormats(char const*, char const*)' CMakeFiles/mychem-lib.dir/modification_wrapper.cpp.o: In functionob_strip_salts':
/home/Aspirin/Downloads/mychem-0.9.3/src/modification_wrapper.cpp:120: undefined reference to OpenBabel::OBConversion::SetInAndOutFormats(char const*, char const*)' CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In functiongetMolWeight':
/home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:68: undefined reference to OpenBabel::OBConversion::SetInFormat(char const*)' CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In functiongetExactMass':
/home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:92: undefined reference to OpenBabel::OBConversion::SetInFormat(char const*)' CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In functiongetAtomCount':
/home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:116: undefined reference to OpenBabel::OBConversion::SetInFormat(char const*)' CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In functiongetHeavyAtomCount':
/home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:140: undefined reference to OpenBabel::OBConversion::SetInFormat(char const*)' CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In functiongetBondCount':
/home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:164: undefined reference to OpenBabel::OBConversion::SetInFormat(char const*)' CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o:/home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:188: more undefined references toOpenBabel::OBConversion::SetInFormat(char const)' follow
CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In function getRotableBondCount': /home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:190: undefined reference toOpenBabel::OBMol::NumRotors()'
CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In function getTotalCharge': /home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:212: undefined reference toOpenBabel::OBConversion::SetInFormat(char const)'
CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In function getFormula': /home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:237: undefined reference toOpenBabel::OBConversion::SetInFormat(char const)'
CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In function getAcceptors': /home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:262: undefined reference toOpenBabel::OBConversion::SetInFormat(char const)'
CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In function getDonors': /home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:292: undefined reference toOpenBabel::OBConversion::SetInFormat(char const)'
CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o: In function getPSA': /home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:323: undefined reference toOpenBabel::OBConversion::SetInFormat(char const)'
CMakeFiles/mychem-lib.dir/property_wrapper.cpp.o:/home/Aspirin/Downloads/mychem-0.9.3/src/property_wrapper.cpp:351: more undefined references to OpenBabel::OBConversion::SetInFormat(char const*)' follow CMakeFiles/mychem-lib.dir/serialization.cpp.o: In functionunserializeOBMol(OpenBabel::OBBase, char const, bool)':
/home/Aspirin/Downloads/mychem-0.9.3/src/serialization.cpp:207: undefined reference to `OpenBabel::OBMol::AddAtom(OpenBabel::OBAtom&)'
collect2: error: ld returned 1 exit status
make[2]: [src/libmychem.so.0.9.3] Error 1
make[1]: [src/CMakeFiles/mychem-lib.dir/all] Error 2
make: *** [all] Error 2
[root@aspirin build]#
have new error！！！
[Aspirin@aspirin build]$ cmake .. -- The build type is RelWithDebInfo -- Test module disabled -- Using mysql-config: /usr/bin/mysql_config -- MySQL Version: 5.7.19 -- MySQL Plugin Dir: -- MySQL not found. -- Mychem installation directory: /opt/mychem/lib -- Defining dlhandler source files CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: MYSQL_LIBRARIES_mysqlclient linked by target "mychem-lib" in directory /home/Aspirin/Downloads/mychem-0.9.3/src linked by target "conversion_test" in directory /home/Aspirin/Downloads/mychem-0.9.3/tests linked by target "helper_test" in directory /home/Aspirin/Downloads/mychem-0.9.3/tests linked by target "modification_test" in directory /home/Aspirin/Downloads/mychem-0.9.3/tests linked by target "molmatch_test" in directory /home/Aspirin/Downloads/mychem-0.9.3/tests linked by target "property_test" in directory /home/Aspirin/Downloads/mychem-0.9.3/tests
-- Configuring incomplete, errors occurred! See also "/home/Aspirin/Downloads/mychem-0.9.3/CMakeFiles/CMakeOutput.log". CMake Error: Unable to open check cache file for write. /home/Aspirin/Downloads/mychem-0.9.3/CMakeFiles/cmake.check_cache [Aspirin@aspirin build]$