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#2 OSRA make error

1.0
new
nobody
None
2018-08-14
2018-08-11
karthik r
No

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::__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></int></int></std::__cxx11::basic_string\<char>

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Tickets: #2

Discussion

  • Igor

    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?

     

    • karthik r

      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::__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
      const      )'
      collect2: error: ld returned 1 exit status</char></char,></int,></int,></char></char,></char></std::__cxx11::basic_string\<char,></char></std::__cxx11::basic_string\<char,></char></char,>

      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?

      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></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</
        obmol>

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  • Igor

    Igor - 2018-08-11

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

     

    • karthik r

      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/

      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></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</
        obmol>

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  • Igor

    Igor - 2018-08-13

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

     

    • karthik r

      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.

      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></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</
        obmol>

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      • karthik r

        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.

        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></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

    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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