Getting the error message when running make all install from osra setup
Error Message:
osra_reaction.cpp: In function ‘std::cxx11::string convert_page_to_reaction(const std::vector<std::__cxx11::basic_string<char> >&, const string&, const std::vector<int>&, const std::vector<int>&, std::</int></int></std::__cxx11::basic_string<char>cxx11::string, bool)’:
osra_reaction.cpp:56:7: error: ‘shared_ptr’ was not declared in this scope
shared_ptr<obmol> reactant(new OBMol);
^
osra_reaction.cpp:56:7: note: suggested alternative:
In file included from /usr/include/c++/5/tr1/memory:50:0,
from /usr/local/include/openbabel-2.0/openbabel/shared_ptr.h:2 ,
from /usr/local/include/openbabel-2.0/openbabel/reaction.h:23,
from osra_reaction.cpp:27:
/usr/include/c++/5/tr1/shared_ptr.h:503:11: note: ‘std::tr1::shared_ptr’
class shared_ptr;
^
osra_reaction.cpp:56:23: error: expected primary-expression before ‘>’ token
shared_ptr<obmol> reactant(new OBMol);
^
osra_reaction.cpp:56:43: error: ‘reactant’ was not declared in this scope
shared_ptr<obmol> reactant(new OBMol);
^
osra_reaction.cpp:62:7: error: ‘shared_ptr’ was not declared in this scope
shared_ptr<obmol> product(new OBMol);
^
osra_reaction.cpp:62:7: note: suggested alternative:
In file included from /usr/include/c++/5/tr1/memory:50:0,
from /usr/local/include/openbabel-2.0/openbabel/shared_ptr.h:2 ,
from /usr/local/include/openbabel-2.0/openbabel/reaction.h:23,
from osra_reaction.cpp:27:
/usr/include/c++/5/tr1/shared_ptr.h:503:11: note: ‘std::tr1::shared_ptr’
class shared_ptr;
^
osra_reaction.cpp:62:23: error: expected primary-expression before ‘>’ token
shared_ptr<obmol> product(new OBMol);
^
osra_reaction.cpp:62:42: error: ‘product’ was not declared in this scope
shared_ptr<obmol> product(new OBMol);
^
<builtin>: recipe for target 'osra_reaction.o' failed
make[2]: [osra_reaction.o] Error 1
make[2]: Leaving directory '/home/developer/osra_package/osra-2.0.0/src'
Makefile:40: recipe for target 'all' failed
make[1]: [all] Error 2
make[1]: Leaving directory '/home/developer/osra_package/osra-2.0.0/src'
Makefile:17: recipe for target 'all.subdir' failed
make: *** [all.subdir] Error 2</builtin></obmol></obmol></obmol></obmol></obmol></obmol>
This issue should be fixed in svn, are you trying to build the code from svn checkout or downloaded the tar.gz file?
Hi Igor
I used openbabel-2.3.2-tr1-memory.tgz, now i am not getting that error, but
this error is coming after make all install. kindly help me to fix this
issue, i am using osra-2.0.0
Error:
osra_openbabel.o: In function
osra_openbabel_init()': /home/developer/osra_package/osra-2.0.0/src/osra_openbabel.cpp:57: undefined reference to
OpenBabel::OBConversion::SetInFormat(char const)'osra_openbabel.o: In function
create_atom(OpenBabel::OBMol&, atom_s&, double, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&, bool)': /home/developer/osra_package/osra-2.0.0/src/osra_openbabel.cpp:99: undefined reference to
OpenBabel::OBConversion::SetInFormat(char const)'osra_openbabel.o: In function
create_molecule(OpenBabel::OBMol&, std::vector<atom_s, std::allocator<atom_s> >&, std::vector<bond_s, std::allocator<bond_s> > const&, int, double, molecule_statistics_s&, bool, double*, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, bool)': /home/developer/osra_package/osra-2.0.0/src/osra_openbabel.cpp:418: undefined reference to
OpenBabel::OBMol::NumRotors()'osra_openbabel.o: In function
get_formatted_structure(std::vector<atom_s, std::allocator<atom_s> >&, std::vector<bond_s, std::allocator<bond_s> > const&, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, molecule_statistics_s&, double&, bool, double, double, bool, int const*, int const*, box_s const*, std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > > const&, int, bool, int, bool)': /home/developer/osra_package/osra-2.0.0/src/osra_openbabel.cpp:686: undefined reference to
OpenBabel::OBConversion::SetOutFormat(char const)'/home/developer/osra_package/osra-2.0.0/src/osra_openbabel.cpp:658:
undefined reference to
OpenBabel::OBConversion::SetOutFormat(char const*)' mcdlutil.o: In function
OpenBabel::TemplateRedraw::loadTemplates()':/home/developer/osra_package/osra-2.0.0/src/mcdlutil.cpp:5864: undefined
reference to
OpenBabel::OBConversion::SetInFormat(char const*)' mcdlutil.o: In function
OpenBabel::addFragment(OpenBabel::OBMol,OpenBabel::OBMol, int, int, int, int, bool)':
/home/developer/osra_package/osra-2.0.0/src/mcdlutil.cpp:7124: undefined
reference to
OpenBabel::OBMol::AddAtom(OpenBabel::OBAtom&)' osra_reaction.o: In function
convert_to_smiles_agent_structure(std::cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&)':/home/developer/osra_package/osra-2.0.0/src/osra_reaction.cpp:89: undefined
reference to
OpenBabel::OBConversion::SetInAndOutFormats(char const*, char const*)' osra_reaction.o: In function
convert_page_to_reaction(std::vector<std::__cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> >,std::allocator<std::__cxx11::basic_string<char, std::char_traits<char="">,
std::allocator<char> > > > const&, std::</char></std::__cxx11::basic_string<char,></char></std::__cxx11::basic_string<char,></char></char,>cxx11::basic_string<char, std::char_traits<char="">, std::allocator<char> > const&, std::vector<int, std::allocator<int=""> > const&, std::vector<int, std::allocator<int=""> >
const&, std::__cxx11::basic_string<char, std::char_traits<char="">,
std::allocator<char> >, bool)':
/home/developer/osra_package/osra-2.0.0/src/osra_reaction.cpp:50: undefined
reference to `OpenBabel::OBConversion::SetInAndOutFormats(char const</char></char,></int,></int,></char></char,>, char
const*)'
collect2: error: ld returned 1 exit status
On Sat, Aug 11, 2018 at 11:16 PM, Igor igor_filippov@users.sourceforge.net
wrote:
Related
Tickets: #2
Also see this support request - seems like the same problem:
https://sourceforge.net/p/osra/support-requests/7/
Hi igor
Thanks for your reply, i checked the source forge ticket so the problem i
need to use openbabel-2.3.2-tr1-memory.tgz , also provide the svn checkout
code or link to access, currently i am using tar.gz file.
On Sat, Aug 11, 2018 at 10:51 AM, Igor igor_filippov@users.sourceforge.net
wrote:
Related
Tickets: #2
Why are you building version 2.0.0? It is 5 years old.
Try a more recent version.
Hi igor
I also tried with osra-2.1.0-1, the same error is coming, kindly help me to
fix the issue.
On Mon, Aug 13, 2018 at 6:03 PM, Igor igor_filippov@users.sourceforge.net
wrote:
Related
Tickets: #2
Hi Igor
Any update please, is it a problem with openbabel installation or kindly
send some steps to compile openbabel, i followed the documentation
https://openbabel.org/docs/dev/Installation/install.html
On Mon, Aug 13, 2018 at 7:47 PM, karthik rajan karthikrajender@gmail.com
wrote:
Related
Tickets: #2
The build instructions are included with OSRA source in README.txt.
They are also available from OSRA website, but the README should correspond to the specific version of OSRA.