Hello:
I tried to follow the instructions posted here:
https://ambermd.org/InstMacOS.php
and in the Amber 2021 Amber Manual.
I am trying to install Amber2022 and AmberTools2021.
Here is the info on the installation tools I am using:
Xcode-select version 2397
gcc installed via brew:
Gcc 13.1.0
cmake version 3.26.3
Next, I am running:
./run_cmake works fine
The only thing noteworthy is that there is no module _distutils_hack
Then I am running:
make install
Here are the last lines (up to this point no errors occurred):
In file included from /Applications/amber/amber20_src/AmberTools/src/pytraj/../cpptraj/src/ParameterSet.h:4:
/Applications/amber/amber20_src/AmberTools/src/pytraj/../cpptraj/src/ParameterHolders.h:200:13: warning: 'typename' occurs outside of a template [-Wc++11-extensions]
typedef typename Bmap::const_iterator const_iterator;
^~~~~~~~~
pytraj/topology/topology.cpp:34820:5: error: expression is not assignable
++Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:34822:5: error: expression is not assignable
--Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:35176:5: error: expression is not assignable
++Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:35178:5: error: expression is not assignable
--Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:36327:5: error: expression is not assignable
++Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:36329:5: error: expression is not assignable
--Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:36638:5: error: expression is not assignable
++Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:36640:5: error: expression is not assignable
--Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:36888:5: error: expression is not assignable
++Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:36890:5: error: expression is not assignable
--Py_REFCNT(o);
^ ~~~~~~~~~~~~
pytraj/topology/topology.cpp:39677:22: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
PyUnicode_WSTR_LENGTH(op) : \
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39677:22: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39677:22: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
PyUnicode_WSTR_LENGTH(op)))
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39677:52: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
PyUnicode_WSTR_LENGTH(op) : \
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39677:52: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39677:52: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
PyUnicode_WSTR_LENGTH(op)))
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39693:26: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
PyUnicode_WSTR_LENGTH(op) : \
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39693:26: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39693:26: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
PyUnicode_WSTR_LENGTH(op)))
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39693:59: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:261:7: note: expanded from macro 'PyUnicode_GET_SIZE'
PyUnicode_WSTR_LENGTH(op) : \
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39693:59: warning: 'PyUnicode_AsUnicode' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:262:14: note: expanded from macro 'PyUnicode_GET_SIZE'
((void)PyUnicode_AsUnicode(_PyObject_CAST(op)),\
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:580:1: note: 'PyUnicode_AsUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(Py_UNICODE *) PyUnicode_AsUnicode(
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:39693:59: warning: '_PyUnicode_get_wstr_length' is deprecated [-Wdeprecated-declarations]
(PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:264:8: note: expanded from macro 'PyUnicode_GET_SIZE'
PyUnicode_WSTR_LENGTH(op)))
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:451:35: note: expanded from macro 'PyUnicode_WSTR_LENGTH'
#define PyUnicode_WSTR_LENGTH(op) _PyUnicode_get_wstr_length((PyObject*)op)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:445:1: note: '_PyUnicode_get_wstr_length' has been explicitly marked deprecated here
Py_DEPRECATED(3.3)
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:41876:16: warning: 'PyUnicode_FromUnicode' is deprecated [-Wdeprecated-declarations]
return PyUnicode_FromUnicode(NULL, 0);
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/cpython/unicodeobject.h:551:1: note: 'PyUnicode_FromUnicode' has been explicitly marked deprecated here
Py_DEPRECATED(3.3) PyAPI_FUNC(PyObject*) PyUnicode_FromUnicode(
^
/Applications/amber/amber20_src/build/CMakeFiles/miniconda/install/include/python3.10/pyport.h:513:54: note: expanded from macro 'Py_DEPRECATED'
#define Py_DEPRECATED(VERSION_UNUSED) __attribute__((__deprecated__))
^
pytraj/topology/topology.cpp:46265:19: error: use of undeclared identifier '_PyGen_Send'
ret = _PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
^
pytraj/topology/topology.cpp:46270:19: error: use of undeclared identifier '_PyGen_Send'
ret = _PyGen_Send((PyGenObject*)yf, value == Py_None ? NULL : value);
^
pytraj/topology/topology.cpp:46354:19: error: use of undeclared identifier '_PyGen_Send'
ret = _PyGen_Send((PyGenObject*)yf, NULL);
^
14 warnings and 13 errors generated.
error: command '/usr/bin/clang' failed with exit code 1
make[2]: *** [AmberTools/src/pytraj/CMakeFiles/python-build/pytraj-build.stamp] Error 1
make[1]: *** [AmberTools/src/pytraj/CMakeFiles/pytraj.dir/all] Error 2
make: *** [all] Error 2
Your help is greatly appreciated,
Markus
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Received on Tue May 02 2023 - 12:30:02 PDT
