dbOutWriter error during basic install

[Evert-Homan]

Hi, I am trying to compile this under Debian running on WSL2. OpenBabel 3 appears to be correctly recognized yet I seem to get these OpenBabel-related errors:

error: expected primary-expression before ‘>’ token 166 | std::unique_ptr<OpenBabel::OBConversion> dbOutWriter( | ^ /home/evehom/shape-it/src/main.cpp:166:44: error: ‘dbOutWriter’ was not declared in this scope 166 | std::unique_ptr<OpenBabel::OBConversion> dbOutWriter(

See complete install log below.

Any pointers to get it working appreciated. BW/Evert

evehom@everthodell:~$ git clone https://github.com/rdkit/shape-it.git Cloning into 'shape-it'... remote: Enumerating objects: 362, done. remote: Counting objects: 100% (362/362), done. remote: Compressing objects: 100% (137/137), done. remote: Total 362 (delta 243), reused 322 (delta 217), pack-reused 0 Receiving objects: 100% (362/362), 160.46 KiB | 1.71 MiB/s, done. Resolving deltas: 100% (243/243), done. evehom@everthodell:~$ cd shape-it/ evehom@everthodell:~/shape-it$ mkdir build evehom@everthodell:~/shape-it$ cd build/ evehom@everthodell:~/shape-it/build$ cmake .. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Open Babel include files at /usr/local/include/openbabel3 -- Found Open Babel library at /usr/local/lib/libopenbabel.so Setting openbabel found TRUE Installation directory of executable: /usr/local/bin -- Configuring done -- Generating done -- Build files have been written to: /home/evehom/shape-it/build evehom@everthodell:~/shape-it/build$ make [ 5%] Building CXX object CMakeFiles/shapeit_lib.dir/src/alignLib.cpp.o [ 11%] Building CXX object CMakeFiles/shapeit_lib.dir/src/alignmentInfo.cpp.o [ 16%] Building CXX object CMakeFiles/shapeit_lib.dir/src/atomGaussian.cpp.o [ 22%] Building CXX object CMakeFiles/shapeit_lib.dir/src/bestResults.cpp.o [ 27%] Building CXX object CMakeFiles/shapeit_lib.dir/src/coordinate.cpp.o [ 33%] Building CXX object CMakeFiles/shapeit_lib.dir/src/gaussianVolume.cpp.o In file included from /usr/local/include/openbabel3/openbabel/atom.h:35, from /home/evehom/shape-it/src/gaussianVolume.cpp:38: /usr/local/include/openbabel3/openbabel/math/vector3.h: In member function ‘bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const’: /usr/local/include/openbabel3/openbabel/math/vector3.h:281:29: warning: ‘bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const’ is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] 281 | return ! ( (*this) == other ); | ^~~~~ /usr/local/include/openbabel3/openbabel/math/vector3.h:274:10: note: declared here 274 | bool operator== ( const vector3& ) const; | ^~~~~~~~ [ 38%] Building CXX object CMakeFiles/shapeit_lib.dir/src/moleculeRotation.cpp.o In file included from /usr/local/include/openbabel3/openbabel/atom.h:35, from /home/evehom/shape-it/src/moleculeRotation.cpp:38: /usr/local/include/openbabel3/openbabel/math/vector3.h: In member function ‘bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const’: /usr/local/include/openbabel3/openbabel/math/vector3.h:281:29: warning: ‘bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const’ is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] 281 | return ! ( (*this) == other ); | ^~~~~ /usr/local/include/openbabel3/openbabel/math/vector3.h:274:10: note: declared here 274 | bool operator== ( const vector3& ) const; | ^~~~~~~~ [ 44%] Building CXX object CMakeFiles/shapeit_lib.dir/src/shapeAlignment.cpp.o [ 50%] Building CXX object CMakeFiles/shapeit_lib.dir/src/siMath.cpp.o [ 55%] Building CXX object CMakeFiles/shapeit_lib.dir/src/solutionInfo.cpp.o In file included from /usr/local/include/openbabel3/openbabel/math/matrix3x3.h:26, from /usr/local/include/openbabel3/openbabel/math/transform3d.h:23, from /usr/local/include/openbabel3/openbabel/math/spacegroup.h:23, from /usr/local/include/openbabel3/openbabel/generic.h:29, from /home/evehom/shape-it/src/solutionInfo.cpp:38: /usr/local/include/openbabel3/openbabel/math/vector3.h: In member function ‘bool OpenBabel::vector3::operator!=(const OpenBabel::vector3&) const’: /usr/local/include/openbabel3/openbabel/math/vector3.h:281:29: warning: ‘bool OpenBabel::vector3::operator==(const OpenBabel::vector3&) const’ is deprecated: Use vector3::IsApprox() instead. [-Wdeprecated-declarations] 281 | return ! ( (*this) == other ); | ^~~~~ /usr/local/include/openbabel3/openbabel/math/vector3.h:274:10: note: declared here 274 | bool operator== ( const vector3& ) const; | ^~~~~~~~ [ 61%] Linking CXX shared library libshapeit_lib.so [ 61%] Built target shapeit_lib [ 66%] Building CXX object CMakeFiles/shape-it.dir/src/options.cpp.o [ 72%] Building CXX object CMakeFiles/shape-it.dir/src/main.cpp.o /home/evehom/shape-it/src/main.cpp: In function ‘int main(int, char**)’: /home/evehom/shape-it/src/main.cpp:166:8: error: ‘unique_ptr’ is not a member of ‘std’ 166 | std::unique_ptr<OpenBabel::OBConversion> dbOutWriter( | ^~~~~~~~~~ /home/evehom/shape-it/src/main.cpp:64:1: note: ‘std::unique_ptr’ is defined in header ‘<memory>’; did you forget to ‘#include <memory>’? 63 | #include <shapeAlignment.h> +++ |+#include <memory> 64 | /home/evehom/shape-it/src/main.cpp:166:42: error: expected primary-expression before ‘>’ token 166 | std::unique_ptr<OpenBabel::OBConversion> dbOutWriter( | ^ /home/evehom/shape-it/src/main.cpp:166:44: error: ‘dbOutWriter’ was not declared in this scope 166 | std::unique_ptr<OpenBabel::OBConversion> dbOutWriter( | ^~~~~~~~~~~ make[2]: *** [CMakeFiles/shape-it.dir/build.make:90: CMakeFiles/shape-it.dir/src/main.cpp.o] Error 1 make[1]: *** [CMakeFiles/Makefile2:111: CMakeFiles/shape-it.dir/all] Error 2 make: *** [Makefile:146: all] Error 2 evehom@everthodell:~/shape-it/build$

[dww100]

I am getting this issue too.