[package - main-i386-default][science/py-openbabel] Failed for py39-openbabel-3.1.1.1 in build
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Date: Wed, 19 Jul 2023 18:14:36 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p94960070866b_s239597e030/logs/py39-openbabel-3.1.1.1.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p94960070866b_s239597e030
Log:
=>> Building science/py-openbabel
build started at Wed Jul 19 18:13:53 UTC 2023
port directory: /usr/ports/science/py-openbabel
package name: py39-openbabel-3.1.1.1
building for: FreeBSD main-i386-default-job-07 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 i386
maintained by: yuri@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License GPLv2+ accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> py39-openbabel-3.1.1.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[main-i386-default-job-07] Installing pkg-1.20.4...
[main-i386-default-job-07] Extracting pkg-1.20.4: .......... done
===> py39-openbabel-3.1.1.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of py39-openbabel-3.1.1.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2+ accepted by the user
===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2+ accepted by the user
===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building
=> SHA256 Checksum OK for openbabel-3.1.1.1.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2+ accepted by the user
===> Fetching all distfiles required by py39-openbabel-3.1.1.1 for building
===> Extracting for py39-openbabel-3.1.1.1
=> SHA256 Checksum OK for openbabel-3.1.1.1.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for py39-openbabel-3.1.1.1
===========================================================================
=======================<phase: build-depends >============================
===> py39-openbabel-3.1.1.1 depends on executable: swig - not found
<snip>
^
openbabel/openbabel-python_wrap.cpp:36417:77: warning: 'LineSearch' is deprecated: Current code should use LineSearch(double *, double*) instead. [-Wdeprecated-declarations]
arg3 = reinterpret_cast< OpenBabel::vector3 * >(argp3); result = (arg1)->LineSearch(arg2,*arg3);
^
/usr/local/include/openbabel3/openbabel/forcefield.h:1222:5: note: 'LineSearch' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("Current code should use LineSearch(double *, double*) instead.")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
openbabel/openbabel-python_wrap.cpp:37025:45: warning: 'VectorLengthDerivative' is deprecated [-Wdeprecated-declarations]
result = (double)OpenBabel::OBForceField::VectorLengthDerivative(*arg1,*arg2);
^
/usr/local/include/openbabel3/openbabel/forcefield.h:1523:5: note: 'VectorLengthDerivative' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:37071:45: warning: 'VectorAngleDerivative' is deprecated [-Wdeprecated-declarations]
result = (double)OpenBabel::OBForceField::VectorAngleDerivative(*arg1,*arg2,*arg3);
^
/usr/local/include/openbabel3/openbabel/forcefield.h:1539:5: note: 'VectorAngleDerivative' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:37141:45: warning: 'VectorOOPDerivative' is deprecated [-Wdeprecated-declarations]
result = (double)OpenBabel::OBForceField::VectorOOPDerivative(*arg1,*arg2,*arg3,*arg4);
^
/usr/local/include/openbabel3/openbabel/forcefield.h:1556:5: note: 'VectorOOPDerivative' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:37211:45: warning: 'VectorTorsionDerivative' is deprecated [-Wdeprecated-declarations]
result = (double)OpenBabel::OBForceField::VectorTorsionDerivative(*arg1,*arg2,*arg3,*arg4);
^
/usr/local/include/openbabel3/openbabel/forcefield.h:1572:5: note: 'VectorTorsionDerivative' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:40899:47: warning: 'SetDelta' is deprecated: Has no effect. [-Wdeprecated-declarations]
arg2 = static_cast< double >(val2); (arg1)->SetDelta(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail: return NULL; }
^
/usr/local/include/openbabel3/openbabel/rotor.h:428:5: note: 'SetDelta' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("Has no effect.")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
openbabel/openbabel-python_wrap.cpp:40905:85: warning: 'GetDelta' is deprecated: Has no effect. [-Wdeprecated-declarations]
arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (double)(arg1)->GetDelta();
^
/usr/local/include/openbabel3/openbabel/rotor.h:431:5: note: 'GetDelta' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("Has no effect.")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
openbabel/openbabel-python_wrap.cpp:40912:102: warning: 'GetFixedAtoms' is deprecated [-Wdeprecated-declarations]
arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (OpenBabel::OBBitVec *) &(arg1)->GetFixedAtoms();
^
/usr/local/include/openbabel3/openbabel/rotor.h:434:5: note: 'GetFixedAtoms' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:40926:69: warning: 'SetFixedAtoms' is deprecated: See SetFixedBonds [-Wdeprecated-declarations]
arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetFixedAtoms(*arg2); resultobj = SWIG_Py_Void();
^
/usr/local/include/openbabel3/openbabel/rotor.h:437:5: note: 'SetFixedAtoms' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("See SetFixedBonds")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
openbabel/openbabel-python_wrap.cpp:40933:102: warning: 'GetEvalAtoms' is deprecated [-Wdeprecated-declarations]
arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (OpenBabel::OBBitVec *) &(arg1)->GetEvalAtoms();
^
/usr/local/include/openbabel3/openbabel/rotor.h:440:5: note: 'GetEvalAtoms' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:40947:69: warning: 'SetEvalAtoms' is deprecated [-Wdeprecated-declarations]
arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetEvalAtoms(*arg2); resultobj = SWIG_Py_Void();
^
/usr/local/include/openbabel3/openbabel/rotor.h:443:5: note: 'SetEvalAtoms' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:40954:85: warning: 'GetRotAtoms' is deprecated [-Wdeprecated-declarations]
arg1 = reinterpret_cast< OpenBabel::OBRotor * >(argp1); result = (void *)(arg1)->GetRotAtoms();
^
/usr/local/include/openbabel3/openbabel/rotor.h:446:5: note: 'GetRotAtoms' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:40962:72: warning: 'GetResolution' is deprecated: See GetTorsionValues() [-Wdeprecated-declarations]
result = (std::vector< double,std::allocator< double > > *) &(arg1)->GetResolution();
^
/usr/local/include/openbabel3/openbabel/rotor.h:449:5: note: 'GetResolution' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("See GetTorsionValues()")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
openbabel/openbabel-python_wrap.cpp:40973:46: warning: 'SetNumCoords' is deprecated [-Wdeprecated-declarations]
arg2 = static_cast< int >(val2); (arg1)->SetNumCoords(arg2); resultobj = SWIG_Py_Void(); return resultobj; fail:
^
/usr/local/include/openbabel3/openbabel/rotor.h:452:5: note: 'SetNumCoords' has been explicitly marked deprecated here
OB_DEPRECATED
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:37:29: note: expanded from macro 'OB_DEPRECATED'
#define OB_DEPRECATED [[deprecated]]
^
openbabel/openbabel-python_wrap.cpp:41254:81: warning: 'IdentifyEvalAtoms' is deprecated: Not declared. Use Setup() for top-level functionality [-Wdeprecated-declarations]
arg2 = reinterpret_cast< OpenBabel::OBMol * >(argp2); result = (bool)(arg1)->IdentifyEvalAtoms(*arg2);
^
/usr/local/include/openbabel3/openbabel/rotor.h:627:5: note: 'IdentifyEvalAtoms' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("Not declared. Use Setup() for top-level functionality")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
openbabel/openbabel-python_wrap.cpp:41267:69: warning: 'SetFixAtoms' is deprecated: See SetFixedBonds() [-Wdeprecated-declarations]
arg2 = reinterpret_cast< OpenBabel::OBBitVec * >(argp2); (arg1)->SetFixAtoms(*arg2); resultobj = SWIG_Py_Void();
^
/usr/local/include/openbabel3/openbabel/rotor.h:633:5: note: 'SetFixAtoms' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("See SetFixedBonds()")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
openbabel/openbabel-python_wrap.cpp:41274:87: warning: 'HasFixedAtoms' is deprecated: See HasFixedBonds() [-Wdeprecated-declarations]
arg1 = reinterpret_cast< OpenBabel::OBRotorList * >(argp1); result = (bool)(arg1)->HasFixedAtoms();
^
/usr/local/include/openbabel3/openbabel/rotor.h:643:5: note: 'HasFixedAtoms' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("See HasFixedBonds()")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
openbabel/openbabel-python_wrap.cpp:41281:72: warning: 'IgnoreSymmetryRemoval' is deprecated: Currently has no effect [-Wdeprecated-declarations]
arg1 = reinterpret_cast< OpenBabel::OBRotorList * >(argp1); (arg1)->IgnoreSymmetryRemoval(); resultobj = SWIG_Py_Void();
^
/usr/local/include/openbabel3/openbabel/rotor.h:650:5: note: 'IgnoreSymmetryRemoval' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("Currently has no effect")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
In file included from openbabel/openbabel-python_wrap.cpp:3415:
/usr/local/include/openbabel3/openbabel/bond.h:58:15: warning: 'Visit' is deprecated: Use OBBitVec objects instead to be fully thread-safe. [-Wdeprecated-declarations]
class OBAPI OBBond: public OBBase
^
openbabel/openbabel-python_wrap.cpp:4075:46: note: in implicit copy constructor for 'OpenBabel::OBBond' first required here
return traits_from_ptr<Type>::from(new Type(val), 1);
^
openbabel/openbabel-python_wrap.cpp:4094:31: note: in instantiation of member function 'swig::traits_from<OpenBabel::OBBond>::from' requested here
return traits_from<Type>::from(val);
^
openbabel/openbabel-python_wrap.cpp:4662:20: note: in instantiation of function template specialization 'swig::from<OpenBabel::OBBond>' requested here
return swig::from(v);
^
openbabel/openbabel-python_wrap.cpp:4749:9: note: in instantiation of member function 'swig::from_oper<OpenBabel::OBBond>::operator()' requested here
return from(static_cast<const value_type&>(*(base::current)));
^
openbabel/openbabel-python_wrap.cpp:4788:5: note: in instantiation of member function 'swig::SwigPyForwardIteratorClosed_T<std::__wrap_iter<OpenBabel::OBBond *>, OpenBabel::OBBond>::value' requested here
SwigPyIteratorClosed_T(out_iterator curr, out_iterator first, out_iterator last, PyObject *seq)
^
openbabel/openbabel-python_wrap.cpp:4818:16: note: in instantiation of member function 'swig::SwigPyIteratorClosed_T<std::__wrap_iter<OpenBabel::OBBond *>, OpenBabel::OBBond>::SwigPyIteratorClosed_T' requested here
return new SwigPyIteratorClosed_T<OutIter>(current, begin, end, seq);
^
openbabel/openbabel-python_wrap.cpp:6408:20: note: in instantiation of function template specialization 'swig::make_output_iterator<std::__wrap_iter<OpenBabel::OBBond *>>' requested here
return swig::make_output_iterator(self->begin(), self->begin(), self->end(), *PYTHON_SELF);
^
/usr/local/include/openbabel3/openbabel/bond.h:97:7: note: 'Visit' has been explicitly marked deprecated here
OB_DEPRECATED_MSG("Use OBBitVec objects instead to be fully thread-safe.")
^
/usr/local/include/openbabel3/openbabel/babelconfig.h:38:38: note: expanded from macro 'OB_DEPRECATED_MSG'
#define OB_DEPRECATED_MSG(msg) [[deprecated(msg)]]
^
36 warnings and 6 errors generated.
error: command '/usr/bin/cc' failed with exit code 1
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-openbabel