osra / Tickets / #2 OSRA make error

Igor - 2018-08-11

This issue should be fixed in svn, are you trying to build the code from svn checkout or downloaded the tar.gz file?

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- karthik r - 2018-08-13
  
  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 toOpenBabel::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 toOpenBabel::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 toOpenBabel::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 toOpenBabel::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 functionOpenBabel::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 functionOpenBabel::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 functionconvert_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 functionconvert_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:
  
  This issue should be fixed in svn, are you trying to build the code from
  svn checkout or downloaded the tar.gz file?
  
  [tickets:#2] https://sourceforge.net/p/osra/tickets/2/ OSRA make error*
  
  Status: new
  Milestone: 1.0
  Created: Sat Aug 11, 2018 02:13 PM UTC by karthik r
  Last Updated: Sat Aug 11, 2018 02:13 PM UTC
  Owner: nobody
  
  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></std::__cxx11::basic_string<char>
  
  &, const string&, const std::vector<int>&, const std::vector<int>&,
  std::</int></int>*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]:</builtin></obmol></obmol></obmol></obmol></obmol></obmol>
  
  [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
  
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Igor - 2018-08-11

Also see this support request - seems like the same problem:
https://sourceforge.net/p/osra/support-requests/7/

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- karthik r - 2018-08-12
  
  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:
  
  Also see this support request - seems like the same problem:
  https://sourceforge.net/p/osra/support-requests/7/
  
  [tickets:#2] https://sourceforge.net/p/osra/tickets/2/ OSRA make error*
  
  Status: new
  Milestone: 1.0
  Created: Sat Aug 11, 2018 02:13 PM UTC by karthik r
  Last Updated: Sat Aug 11, 2018 05:46 PM UTC
  Owner: nobody
  
  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></std::__cxx11::basic_string<char>
  
  &, const string&, const std::vector<int>&, const std::vector<int>&,
  std::</int></int>*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]:</builtin></obmol></obmol></obmol></obmol></obmol></obmol>
  
  [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
  
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Igor - 2018-08-13

Why are you building version 2.0.0? It is 5 years old.
Try a more recent version.

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- karthik r - 2018-08-13
  
  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:
  
  Why are you building version 2.0.0? It is 5 years old.
  Try a more recent version.
  
  [tickets:#2] https://sourceforge.net/p/osra/tickets/2/ OSRA make error*
  
  Status: new
  Milestone: 1.0
  Created: Sat Aug 11, 2018 02:13 PM UTC by karthik r
  Last Updated: Sat Aug 11, 2018 05:51 PM UTC
  Owner: nobody
  
  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></std::__cxx11::basic_string<char>
  
  &, const string&, const std::vector<int>&, const std::vector<int>&,
  std::</int></int>*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]:</builtin></obmol></obmol></obmol></obmol></obmol></obmol>
  
  [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
  
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  - karthik r - 2018-08-14
    
    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:
    
    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:
    
    Why are you building version 2.0.0? It is 5 years old.
    Try a more recent version.
    
    [tickets:#2] https://sourceforge.net/p/osra/tickets/2/ OSRA make
    error*
    
    Status: new
    Milestone: 1.0
    Created: Sat Aug 11, 2018 02:13 PM UTC by karthik r
    Last Updated: Sat Aug 11, 2018 05:51 PM UTC
    Owner: nobody
    
    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></std::__cxx11::basic_string<char>
    
    &, const string&, const std::vector<int>&, const std::vector<int>&,
    std::</int></int>*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]:</builtin></obmol></obmol></obmol></obmol></obmol></obmol>
    
    [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
    
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Igor - 2018-08-14

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.

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OSRA make error

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