[package - 124i386-quarterly][science/py-openbabel] Failed for py39-openbabel-3.1.1.1 in build
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Date: Tue, 22 Aug 2023 19:35:16 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/beefy4/data/124i386-quarterly/f3d8c4bf5c40/logs/py39-openbabel-3.1.1.1.log
Build URL: https://pkg-status.freebsd.org/beefy4/build.html?mastername=124i386-quarterly&build=f3d8c4bf5c40
Log:
=>> Building science/py-openbabel
build started at Tue Aug 22 19:33:45 UTC 2023
port directory: /usr/ports/science/py-openbabel
package name: py39-openbabel-3.1.1.1
building for: FreeBSD 124i386-quarterly-job-01 12.4-RELEASE-p4 FreeBSD 12.4-RELEASE-p4 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-1.19.2.pkg
[124i386-quarterly-job-01] Installing pkg-1.19.2...
[124i386-quarterly-job-01] Extracting pkg-1.19.2: .......... 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
===> Installing existing package /packages/All/swig-4.1.1.pkg
[124i386-quarterly-job-01] Installing swig-4.1.1...
[124i386-quarterly-job-01] `-- Installing pcre2-10.42...
[124i386-quarterly-job-01] `-- Extracting pcre2-10.42: .......... done
[124i386-quarterly-job-01] Extracting swig-4.1.1: .......... done
===> py39-openbabel-3.1.1.1 depends on executable: swig - found
===> Returning to build of py39-openbabel-3.1.1.1
===> py39-openbabel-3.1.1.1 depends on package: py39-setuptools>=63.1.0 - not found
===> Installing existing package /packages/All/py39-setuptools-63.1.0_1.pkg
[124i386-quarterly-job-01] Installing py39-setuptools-63.1.0_1...
[124i386-quarterly-job-01] `-- Installing python39-3.9.17...
[124i386-quarterly-job-01] | `-- Installing gettext-runtime-0.21.1...
<snip>
#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)]]
^
PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script.
Stack dump:
0. Program arguments: /usr/bin/cc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/usr/local/include/python3.9 -I/usr/local/include/openbabel3 -c openbabel/openbabel-python_wrap.cpp -o build/temp.freebsd-12.4-RELEASE-p4-i386-cpython-39/openbabel/openbabel-python_wrap.o
1. <eof> parser at end of file
2. Code generation
3. Running pass 'Function Pass Manager' on module 'openbabel/openbabel-python_wrap.cpp'.
4. Running pass 'X86 DAG->DAG Instruction Selection' on function '@_Z11toAliasDataPN9OpenBabel13OBGenericDataE'
#0 0x049f5de4 (/usr/bin/cc+0x49f5de4)
#1 0x049f62c0 (/usr/bin/cc+0x49f62c0)
#2 0x049f40ae (/usr/bin/cc+0x49f40ae)
#3 0x049f8103 (/usr/bin/cc+0x49f8103)
#4 0x05b70969 (/usr/bin/cc+0x5b70969)
cc: error: clang frontend command failed with exit code 139 (use -v to see invocation)
FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303)
Target: i386-unknown-freebsd12.4
Thread model: posix
InstalledDir: /usr/bin
cc: note: diagnostic msg:
********************
PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
cc: note: diagnostic msg: /tmp/openbabel-python_wrap-19585f.cpp
cc: note: diagnostic msg: /tmp/openbabel-python_wrap-19585f.sh
cc: note: diagnostic msg:
********************
error: command '/usr/bin/cc' failed with exit code 139
*** Error code 1
Stop.
make: stopped in /usr/ports/science/py-openbabel