fredrikw
commented
6 years ago Now it looks like a problem with the OpenBabel installation. How did you install that? The error messages indicate that it can find the header files, but not the library.
Closed AspirinCode closed 1 year ago
fredrikw
commented
6 years ago Now it looks like a problem with the OpenBabel installation. How did you install that? The error messages indicate that it can find the header files, but not the library.
AspirinCode
commented
6 years ago compiled and installed OpenBabel2.4.1
fredrikw
commented
6 years ago What did the CMake log say about OpenBabel? You could try to specify the locations of OpenBabel to CMake. I usually use ccmake to get a list of all settings and make sure that they are correct.
Pansanel
commented
6 years ago I did not test mychem against OpenBabel v2.4.1. Some files may need an update. I will check this asap!
prfsullivan
commented
6 years ago Hello, I'd really appreciate the help. I'm having a similar but somewhat different issue. After applying the 'make' command, I get this message:
10-124-219-136:build petersullivan$ make
Scanning dependencies of target mychem-lib
[ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:46:
/usr/local/include/mysql/my_global.h:3:2: warning: This file should not be included by clients, include only
^
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:47:
/usr/local/include/mysql/my_sys.h:3:2: warning: This file should not be included by clients, include only
^
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:49:
/usr/local/include/mysql/m_ctype.h:43:3: error: unknown type name 'uint16'; did you mean 'uint'?
uint16 toupper;
^~
uint
/usr/include/sys/types.h:92:23: note: 'uint' declared here
typedef unsigned int uint; / Sys V compatibility /
^
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:49:
/usr/local/include/mysql/m_ctype.h:44:3: error: unknown type name 'uint16'; did you mean 'uint'?
uint16 tolower;
^~
uint
/usr/include/sys/types.h:92:23: note: 'uint' declared here
typedef unsigned int uint; / Sys V compatibility /
^
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:49:
/usr/local/include/mysql/m_ctype.h:45:3: error: unknown type name 'uint16'; did you mean 'uint'?
uint16 sort;
^~
uint
/usr/include/sys/types.h:92:23: note: 'uint' declared here
typedef unsigned int uint; / Sys V compatibility /
^
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:49:
/usr/local/include/mysql/m_ctype.h:54:3: error: unknown type name 'uchar'
uchar pctype;
^
/usr/local/include/mysql/m_ctype.h:55:3: error: unknown type name 'uchar'
uchar ctype;
^
/usr/local/include/mysql/m_ctype.h:100:3: error: unknown type name 'uint16'; did you mean 'uint'?
uint16 from;
^~
uint
/usr/include/sys/types.h:92:23: note: 'uint' declared here
typedef unsigned int uint; / Sys V compatibility /
^
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:49:
/usr/local/include/mysql/m_ctype.h:101:3: error: unknown type name 'uint16'; did you mean 'uint'?
uint16 to;
^~
uint
/usr/include/sys/types.h:92:23: note: 'uint' declared here
typedef unsigned int uint; / Sys V compatibility /
^
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:49:
/usr/local/include/mysql/m_ctype.h:102:3: error: unknown type name 'uchar'
uchar tab;
^
/usr/local/include/mysql/m_ctype.h:137:16: error: unknown type name 'uchar'
const uchar , size_t, const uchar , size_t, my_bool);
^
/usr/local/include/mysql/m_ctype.h:137:39: error: unknown type name 'uchar'
const uchar , size_t, const uchar , size_t, my_bool);
^
/usr/local/include/mysql/m_ctype.h:139:32: error: unknown type name 'uchar'
const uchar , size_t, const uchar , size_t,
^
/usr/local/include/mysql/m_ctype.h:139:55: error: unknown type name 'uchar'
const uchar , size_t, const uchar , size_t,
^
/usr/local/include/mysql/m_ctype.h:142:26: error: unknown type name 'uchar'
uchar , size_t, const uchar , size_t);
^
/usr/local/include/mysql/m_ctype.h:142:49: error: unknown type name 'uchar'
uchar , size_t, const uchar , size_t);
^
/usr/local/include/mysql/m_ctype.h:146:4: error: unknown type name 'pchar'; did you mean 'char'?
pchar w_prefix, pchar w_one, pchar w_many,
^~~~~
char
/usr/local/include/mysql/m_ctype.h:146:20: error: unknown type name 'pchar'; did you mean 'char'?
pchar w_prefix, pchar w_one, pchar w_many,
^~~~~
char
/usr/local/include/mysql/m_ctype.h:146:33: error: unknown type name 'pchar'; did you mean 'char'?
pchar w_prefix, pchar w_one, pchar w_many,
^~~~~
char
/usr/local/include/mysql/m_ctype.h:163:55: error: unknown type name 'uchar'
void (hash_sort)(struct charset_info_st cs, const uchar key, size_t len,
^
/usr/local/include/mysql/m_ctype.h:164:7: error: unknown type name 'ulong'
ulong nr1, ulong *nr2);
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
2 warnings and 20 errors generated.
make[2]: [src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1
make[1]: [src/CMakeFiles/mychem-lib.dir/all] Error 2
make: *** [all] Error 2
10-124-219-136:build petersullivan$ make
Scanning dependencies of target mychem-lib
[ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:46:
/usr/local/include/mysql/my_global.h:484:10: fatal error: 'my_compiler.h' file not found
^~~~~~~~~~~~~~~1 error generated.
make[2]: [src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1
make[1]: [src/CMakeFiles/mychem-lib.dir/all] Error 2
make: *** [all] Error 2
10-124-219-136:build petersullivan$ make
[ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31:
In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:46:
/usr/local/include/mysql/my_global.h:484:10: warning: non-portable path to file '
^~~~~~~~~~~~~~~
<My_compiler.h>In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31: In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:46: In file included from /usr/local/include/mysql/my_global.h:484: /usr/local/include/mysql/my_compiler.h:1493:1: error: non-ASCII characters are not allowed outside of literals and identifiers © 2018 GitHub, Inc. ^~ /usr/local/include/mysql/my_compiler.h:1493:4: error: expected identifier or '(' © 2018 GitHub, Inc. ^ In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31: In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:46: /usr/local/include/mysql/my_global.h:545:9: error: unknown type name 'SOCKET_SIZE_TYPE' typedef SOCKET_SIZE_TYPE size_socket; ^ /usr/local/include/mysql/my_global.h:722:2: error: "please add -DSTACK_DIRECTION=1 or -1 to your CPPFLAGS"
^ /usr/local/include/mysql/my_global.h:791:9: warning: 'isnan' macro redefined [-Wmacro-redefined]
^/usr/include/math.h:178:9: note: previous definition is here
^In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.c:31: In file included from /Users/petersullivan/Documents/computer-related/MySQL/mychem-code-0.9.3/src/conversion.h:46: /usr/local/include/mysql/my_global.h:1029:10: fatal error: 'my_dbug.h' file not found
^~~~~~~~~~~2 warnings and 5 errors generated. make[2]: [src/CMakeFiles/mychem-lib.dir/conversion.c.o] Error 1 make[1]: [src/CMakeFiles/mychem-lib.dir/all] Error 2 make: *** [all] Error 2
Pansanel
commented
4 years ago Can you share the build/CMakeCache.txt file?
[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]
if (_WIN32)
^ /usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
if (__cplusplus >= 201103L)
^ [ 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 fp, bool bSet=true) ^ /home/Aspirin/Downloads/mychem-0.9.3/src/fingerprints/finger2.cpp:48:21: warning: unused parameter ‘bSet’ [-Wunused-parameter] In file included from /home/Aspirin/Downloads/mychem-0.9.3/src/conversion_wrapper.cpp:41:0: /home/Aspirin/Downloads/mychem-0.9.3/src/fingerprints/finger3.cpp: In member function ‘virtual bool OpenBabel::PatternFP::GetFingerprint(OpenBabel::OBBase*, std::vector&, int)’: /home/Aspirin/Downloads/mychem-0.9.3/src/fingerprints/finger3.cpp:93:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] while(n < _bitcount) ^ /home/Aspirin/Downloads/mychem-0.9.3/src/fingerprints/finger3.cpp: In member function ‘virtual std::string OpenBabel::PatternFP::DescribeBits(std::vector, bool)’: /home/Aspirin/Downloads/mychem-0.9.3/src/fingerprints/finger3.cpp:220:36: warning: operation on ‘div’ may be undefined [-Wsequence-point] ngrp = (num + div -1)/div--; //rounds up ^ [ 11%] Building C object src/CMakeFiles/mychem-lib.dir/helper.c.o In file included from /home/Aspirin/Downloads/mychem-0.9.3/src/helper.h:45:0, from /home/Aspirin/Downloads/mychem-0.9.3/src/helper.c:31: /usr/local/mysql/include/my_global.h:362:6: warning: "_WIN32" is not defined [-Wundef]
if (_WIN32)
^ /usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
if (__cplusplus >= 201103L)
^ [ 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]
if (_WIN32)
^ /usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
if (__cplusplus >= 201103L)
^ [ 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]
if (_WIN32)
^ /usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
if (__cplusplus >= 201103L)
^ [ 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]
if (_WIN32)
^ /usr/local/mysql/include/my_global.h:417:6: warning: "__cplusplus" is not defined [-Wundef]
if (__cplusplus >= 201103L)
^ [ 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！！！