atomic_lib compilation warning "ChimeraX_main.py: option -I not recognized"

[Tom Goddard]

make install on atomic_lib on macOS 10.15 gives strange warnings about -I option not recognized by ChimeraX_main.py.

cd src/bundles/atomic_lib
$ make install
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/bin/ChimeraX --nogui --safemode --exit --cmd "devel install . user false exit true noDeps true"
0.00% done: Initializing core
50.00% done: Initializing bundles
Executing: devel install . user false exit true noDeps true
Warning: Can't read registry to find the necessary compiler setting
Make sure that Python modules winreg, win32api or win32con are installed.
C compiler: clang -pipe -DUSE_DYLD_GLOBAL_NAMESPACE -fno-strict-aliasing -Wsign-compare -Wunreachable-code -fno-common -dynamic -F/Users/goddard/ucsf/chimerax/build/Library/Frameworks -DNDEBUG -g -fwrapv -O3 -Wall

compile options: '-std=c++11 -stdlib=libc++ -DDYNAMIC_LIBRARY=1 -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c'
clang: atomic_cpp/pyinstance_cpp/PythonInstance.cpp
c++ -pipe -I/Users/goddard/ucsf/chimerax/build/include -L/Users/goddard/ucsf/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -dynamiclib -undefined dynamic_lookup -O3 -Wall -Wextra -F/Users/goddard/ucsf/chimerax/build/Library/Frameworks -Wl,-rpath,@loader_path -Wl,-install_name,@rpath/libpyinstance.dylib atomic_cpp/pyinstance_cpp/PythonInstance.o -L/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/lib -L/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/lib -o src/lib/libpyinstance.dylib
C compiler: clang -pipe -DUSE_DYLD_GLOBAL_NAMESPACE -fno-strict-aliasing -Wsign-compare -Wunreachable-code -fno-common -dynamic -F/Users/goddard/ucsf/chimerax/build/Library/Frameworks -DNDEBUG -g -fwrapv -O3 -Wall

compile options: '-std=c++11 -stdlib=libc++ -DDYNAMIC_LIBRARY=1 -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/include -Isrc/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c'
clang: atomic_cpp/element_cpp/Element.cpp
c++ -pipe -I/Users/goddard/ucsf/chimerax/build/include -L/Users/goddard/ucsf/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -dynamiclib -undefined dynamic_lookup -O3 -Wall -Wextra -F/Users/goddard/ucsf/chimerax/build/Library/Frameworks -Wl,-rpath,@loader_path -Wl,-install_name,@rpath/libelement.dylib atomic_cpp/element_cpp/Element.o -L/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/lib -Lsrc/lib -L/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/lib -lpyinstance -o src/lib/libelement.dylib
C compiler: clang -pipe -DUSE_DYLD_GLOBAL_NAMESPACE -fno-strict-aliasing -Wsign-compare -Wunreachable-code -fno-common -dynamic -F/Users/goddard/ucsf/chimerax/build/Library/Frameworks -DNDEBUG -g -fwrapv -O3 -Wall

compile options: '-std=c++11 -stdlib=libc++ -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/include -Isrc/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c'
clang: atomic_cpp/atomstruct_cpp/tmpl/Atom.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/CoordSet.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/Bond.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/Molecule.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/Residue.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/TemplateCache.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/amino.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/camino.cpp
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py: option -I not recognized
Usage: /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py [--debug] [--exit] [--nogui] [--nocolor] [--help] [--lineprofile] [--listioformats] [--offscreen] [--silent] [--nostatus] [--start <tool name>] [--cmd <command>] [--script <python script and arguments>] [--notools] [--safemode] [--stereo] [--uninstall] [--usedefaults] [--version] [--qtscalefactor <factor>] [--toolshed preview|<url>] or -m module_name [args] or -c command [args] or -u -c command [args]

clang: atomic_cpp/atomstruct_cpp/tmpl/findres.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/general.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/ions.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/namino.cpp
clang: atomic_cpp/atomstruct_cpp/tmpl/nucleic.cpp
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/resource_tracker.py:96: UserWarning: resource_tracker: process died unexpectedly, relaunching. Some resources might leak.

warnings.warn('resource_tracker: process died unexpectedly, '

ar: adding 13 object files to src/lib/libatomstruct_tmpl.a
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py: option -I not recognized
usage: /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py [--debug] [--exit] [--nogui] [--nocolor] [--help] [--lineprofile] [--listioformats] [--offscreen] [--silent] [--nostatus] [--start <tool name>] [--cmd <command>] [--script <python script and arguments>] [--notools] [--safemode] [--stereo] [--uninstall] [--usedefaults] [--version] [--qtscalefactor <factor>] [--toolshed preview|<url>] or -m module_name [args] or -c command [args] or -u -c command [args]

ranlib:@ src/lib/libatomstruct_tmpl.a
C compiler: clang -pipe -DUSE_DYLD_GLOBAL_NAMESPACE -fno-strict-aliasing -Wsign-compare -Wunreachable-code -fno-common -dynamic -F/Users/goddard/ucsf/chimerax/build/Library/Frameworks -DNDEBUG -g -fwrapv -O3 -Wall

compile options: '-std=c++11 -stdlib=libc++ -DDYNAMIC_LIBRARY=1 -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/include -Isrc/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/include -I/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/include/python3.8 -c'
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/resource_tracker.py:96: UserWarning: resource_tracker: process died unexpectedly, relaunching. Some resources might leak.

warnings.warn('resource_tracker: process died unexpectedly, '

clang: atomic_cpp/atomstruct_cpp/Atom.cpp
clang: atomic_cpp/atomstruct_cpp/AtomTypes.cpp
clang: atomic_cpp/atomstruct_cpp/AtomicStructure.cpp
clang: atomic_cpp/atomstruct_cpp/Bond.cpp
clang: atomic_cpp/atomstruct_cpp/Chain.cpp
clang: atomic_cpp/atomstruct_cpp/ChangeTracker.cpp
clang: atomic_cpp/atomstruct_cpp/CompSS.cpp
clang: atomic_cpp/atomstruct_cpp/CoordSet.cpp
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py: option -I not recognized
usage: /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py [--debug] [--exit] [--nogui] [--nocolor] [--help] [--lineprofile] [--listioformats] [--offscreen] [--silent] [--nostatus] [--start <tool name>] [--cmd <command>] [--script <python script and arguments>] [--notools] [--safemode] [--stereo] [--uninstall] [--usedefaults] [--version] [--qtscalefactor <factor>] [--toolshed preview|<url>] or -m module_name [args] or -c command [args] or -u -c command [args]

atomic_cpp/atomstruct_cpp/CompSS.cpp:650:2: warning: misleading indentation; statement is not part of

the previous 'for' [-Wmisleading-indentation]

try {

atomic_cpp/atomstruct_cpp/CompSS.cpp:646:5: note: previous statement is here

for (auto& hbonds: params.hbonds)

clang: atomic_cpp/atomstruct_cpp/MolResId.cpp
clang: atomic_cpp/atomstruct_cpp/PBGroup.cpp
clang: atomic_cpp/atomstruct_cpp/PBManager.cpp
clang: atomic_cpp/atomstruct_cpp/Point.cpp
clang: atomic_cpp/atomstruct_cpp/Pseudobond.cpp
clang: atomic_cpp/atomstruct_cpp/Residue.cpp
1 warning generated.
clang: atomic_cpp/atomstruct_cpp/Ring.cpp
clang: atomic_cpp/atomstruct_cpp/RingCalc.cpp
clang: atomic_cpp/atomstruct_cpp/Sequence.cpp
clang: atomic_cpp/atomstruct_cpp/Structure.cpp
clang: atomic_cpp/atomstruct_cpp/StructureSeq.cpp
clang: atomic_cpp/atomstruct_cpp/destruct.cpp
clang: atomic_cpp/atomstruct_cpp/seq_assoc.cpp
atomic_cpp/atomstruct_cpp/Structure.cpp:639:5: warning: loop will run at most once

(loop increment never executed) [-Wunreachable-code-loop-increment]

for (auto a: r->atoms())

1 warning generated.
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/multiprocessing/resource_tracker.py:96: UserWarning: resource_tracker: process died unexpectedly, relaunching. Some resources might leak.

warnings.warn('resource_tracker: process died unexpectedly, '

c++ -pipe -I/Users/goddard/ucsf/chimerax/build/include -L/Users/goddard/ucsf/chimerax/build/lib -DUSE_DYLD_GLOBAL_NAMESPACE -dynamiclib -undefined dynamic_lookup -O3 -Wall -Wextra -F/Users/goddard/ucsf/chimerax/build/Library/Frameworks -Wl,-rpath,@loader_path -Wl,-install_name,@rpath/libatomstruct.dylib atomic_cpp/atomstruct_cpp/Atom.o atomic_cpp/atomstruct_cpp/AtomTypes.o atomic_cpp/atomstruct_cpp/AtomicStructure.o atomic_cpp/atomstruct_cpp/Bond.o atomic_cpp/atomstruct_cpp/Chain.o atomic_cpp/atomstruct_cpp/ChangeTracker.o atomic_cpp/atomstruct_cpp/CompSS.o atomic_cpp/atomstruct_cpp/CoordSet.o atomic_cpp/atomstruct_cpp/MolResId.o atomic_cpp/atomstruct_cpp/PBGroup.o atomic_cpp/atomstruct_cpp/PBManager.o atomic_cpp/atomstruct_cpp/Point.o atomic_cpp/atomstruct_cpp/Pseudobond.o atomic_cpp/atomstruct_cpp/Residue.o atomic_cpp/atomstruct_cpp/Ring.o atomic_cpp/atomstruct_cpp/RingCalc.o atomic_cpp/atomstruct_cpp/Sequence.o atomic_cpp/atomstruct_cpp/Structure.o atomic_cpp/atomstruct_cpp/StructureSeq.o atomic_cpp/atomstruct_cpp/destruct.o atomic_cpp/atomstruct_cpp/seq_assoc.o -L/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/lib -Lsrc/lib -L/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/chimerax/arrays/lib -lpyinstance -lelement -latomstruct_tmpl -lioutil -lchutil -llogger -larrays -o src/lib/libatomstruct.dylib
/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py: option -I not recognized
usage: /Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-packages/ChimeraX_main.py [--debug] [--exit] [--nogui] [--nocolor] [--help] [--lineprofile] [--listioformats] [--offscreen] [--silent] [--nostatus] [--start <tool name>] [--cmd <command>] [--script <python script and arguments>] [--notools] [--safemode] [--stereo] [--uninstall] [--usedefaults] [--version] [--qtscalefactor <factor>] [--toolshed preview|<url>] or -m module_name [args] or -c command [args] or -u -c command [args]

running build
running build_py
copying src/include/atomstruct/Chain.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Connection.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/MolResId.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/destruct.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/string_types.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/PBManager.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Structure.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Point.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Ring.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/StructureSeq.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/seq_assoc.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Coord.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Real.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/CoordSet.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/backbone.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Atom.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/session.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Sequence.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Residue.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/polymer.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Pseudobond.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Rgba.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/PBGroup.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/imex.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/ChangeTracker.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/AtomicStructure.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/atomstruct/Bond.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct
copying src/include/element/Element.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/element
copying src/include/element/imex.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/element
copying src/include/pyinstance/PythonInstance.instantiate.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/pyinstance
copying src/include/pyinstance/PythonInstance.declare.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/pyinstance
copying src/include/pyinstance/imex.map.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/pyinstance
copying src/include/pyinstance/imex.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/pyinstance
copying src/include/atomstruct/tmpl/resinternal.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/resDescrip.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/TAexcept.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/Molecule.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/Coord.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/TemplateCache.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/CoordSet.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/Atom.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/restmpl.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/Residue.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/residues.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/include/atomstruct/tmpl/Bond.h -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl
copying src/lib/libelement.dylib -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/lib
copying src/lib/libpyinstance.dylib -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/lib
copying src/lib/libatomstruct_tmpl.a -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/lib
copying src/lib/libatomstruct.dylib -> build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/lib
running build_ext
running bdist_wheel
installing to build/bdist.macosx-10.15-x86_64/wheel
running install
running install_lib
running build_ext
creating build/bdist.macosx-10.15-x86_64/wheel
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Chain.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Connection.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/MolResId.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/destruct.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/string_types.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/PBManager.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/resinternal.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/resDescrip.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/TAexcept.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/Molecule.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/Coord.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/TemplateCache.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/CoordSet.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/Atom.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/restmpl.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/Residue.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/residues.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/tmpl/Bond.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct/tmpl
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Structure.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Point.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Ring.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/StructureSeq.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/seq_assoc.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Coord.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Real.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/CoordSet.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/backbone.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Atom.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/session.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Sequence.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Residue.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/polymer.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Pseudobond.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Rgba.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/PBGroup.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/imex.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/ChangeTracker.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/AtomicStructure.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/atomstruct/Bond.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/atomstruct
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/element
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/element/Element.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/element
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/element/imex.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/element
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/pyinstance
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/pyinstance/PythonInstance.instantiate.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/pyinstance
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/pyinstance/PythonInstance.declare.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/pyinstance
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/pyinstance/imex.map.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/pyinstance
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/include/pyinstance/imex.h -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/include/pyinstance
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/init.py -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/lib
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/lib/libelement.dylib -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/lib
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/lib/libpyinstance.dylib -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/lib
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/lib/libatomstruct_tmpl.a -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/lib
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/lib/libatomstruct.dylib -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/lib
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm
creating build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/CYS.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/TRP.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/ALA.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/GLN.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/MSE.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/HIS.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/THR.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/MET.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/DC.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/PHE.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/C.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/ACE.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/SER.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/LYS.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/ARG.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/HYP.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/ASP.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/LEU.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/TYR.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/A.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/GLY.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/HIP.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/DA.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/U.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/T.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/PRO.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/FORMAT -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/DT.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/ASN.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/HID.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/HIE.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/HOH.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/VAL.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/G.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/DG.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/GLU.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/data/idatm/templates/ILE.idatmres -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib/data/idatm/templates
copying build/lib.macosx-10.15-x86_64-3.8/chimerax/atomic_lib/_load_libs.cpython-38-darwin.so -> build/bdist.macosx-10.15-x86_64/wheel/chimerax/atomic_lib
running install_egg_info
running egg_info
writing ChimeraX_AtomicLibrary.egg-info/PKG-INFO
writing dependency_links to ChimeraX_AtomicLibrary.egg-info/dependency_links.txt
writing requirements to ChimeraX_AtomicLibrary.egg-info/requires.txt
writing top-level names to ChimeraX_AtomicLibrary.egg-info/top_level.txt
reading manifest file 'ChimeraX_AtomicLibrary.egg-info/SOURCES.txt'
writing manifest file 'ChimeraX_AtomicLibrary.egg-info/SOURCES.txt'
Copying ChimeraX_AtomicLibrary.egg-info to build/bdist.macosx-10.15-x86_64/wheel/ChimeraX_AtomicLibrary-1.1.1-py3.8.egg-info
running install_scripts
creating build/bdist.macosx-10.15-x86_64/wheel/ChimeraX_AtomicLibrary-1.1.1.dist-info/WHEEL
creating 'dist/ChimeraX_AtomicLibrary-1.1.1-cp38-cp38-macosx_10_15_x86_64.whl' and adding 'build/bdist.macosx-10.15-x86_64/wheel' to it
adding 'chimerax/atomic_lib/init.py'
adding 'chimerax/atomic_lib/_load_libs.cpython-38-darwin.so'
adding 'chimerax/atomic_lib/data/idatm/templates/A.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/ACE.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/ALA.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/ARG.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/ASN.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/ASP.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/C.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/CYS.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/DA.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/DC.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/DG.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/DT.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/FORMAT'
adding 'chimerax/atomic_lib/data/idatm/templates/G.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/GLN.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/GLU.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/GLY.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/HID.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/HIE.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/HIP.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/HIS.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/HOH.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/HYP.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/ILE.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/LEU.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/LYS.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/MET.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/MSE.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/PHE.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/PRO.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/SER.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/T.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/THR.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/TRP.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/TYR.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/U.idatmres'
adding 'chimerax/atomic_lib/data/idatm/templates/VAL.idatmres'
adding 'chimerax/atomic_lib/include/atomstruct/Atom.h'
adding 'chimerax/atomic_lib/include/atomstruct/AtomicStructure.h'
adding 'chimerax/atomic_lib/include/atomstruct/Bond.h'
adding 'chimerax/atomic_lib/include/atomstruct/Chain.h'
adding 'chimerax/atomic_lib/include/atomstruct/ChangeTracker.h'
adding 'chimerax/atomic_lib/include/atomstruct/Connection.h'
adding 'chimerax/atomic_lib/include/atomstruct/Coord.h'
adding 'chimerax/atomic_lib/include/atomstruct/CoordSet.h'
adding 'chimerax/atomic_lib/include/atomstruct/MolResId.h'
adding 'chimerax/atomic_lib/include/atomstruct/PBGroup.h'
adding 'chimerax/atomic_lib/include/atomstruct/PBManager.h'
adding 'chimerax/atomic_lib/include/atomstruct/Point.h'
adding 'chimerax/atomic_lib/include/atomstruct/Pseudobond.h'
adding 'chimerax/atomic_lib/include/atomstruct/Real.h'
adding 'chimerax/atomic_lib/include/atomstruct/Residue.h'
adding 'chimerax/atomic_lib/include/atomstruct/Rgba.h'
adding 'chimerax/atomic_lib/include/atomstruct/Ring.h'
adding 'chimerax/atomic_lib/include/atomstruct/Sequence.h'
adding 'chimerax/atomic_lib/include/atomstruct/Structure.h'
adding 'chimerax/atomic_lib/include/atomstruct/StructureSeq.h'
adding 'chimerax/atomic_lib/include/atomstruct/backbone.h'
adding 'chimerax/atomic_lib/include/atomstruct/destruct.h'
adding 'chimerax/atomic_lib/include/atomstruct/imex.h'
adding 'chimerax/atomic_lib/include/atomstruct/polymer.h'
adding 'chimerax/atomic_lib/include/atomstruct/seq_assoc.h'
adding 'chimerax/atomic_lib/include/atomstruct/session.h'
adding 'chimerax/atomic_lib/include/atomstruct/string_types.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/Atom.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/Bond.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/Coord.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/CoordSet.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/Molecule.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/Residue.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/TAexcept.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/TemplateCache.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/resDescrip.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/residues.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/resinternal.h'
adding 'chimerax/atomic_lib/include/atomstruct/tmpl/restmpl.h'
adding 'chimerax/atomic_lib/include/element/Element.h'
adding 'chimerax/atomic_lib/include/element/imex.h'
adding 'chimerax/atomic_lib/include/pyinstance/PythonInstance.declare.h'
adding 'chimerax/atomic_lib/include/pyinstance/PythonInstance.instantiate.h'
adding 'chimerax/atomic_lib/include/pyinstance/imex.h'
adding 'chimerax/atomic_lib/include/pyinstance/imex.map.h'
adding 'chimerax/atomic_lib/lib/libatomstruct.dylib'
adding 'chimerax/atomic_lib/lib/libatomstruct_tmpl.a'
adding 'chimerax/atomic_lib/lib/libelement.dylib'
adding 'chimerax/atomic_lib/lib/libpyinstance.dylib'
adding 'ChimeraX_AtomicLibrary-1.1.1.dist-info/METADATA'
adding 'ChimeraX_AtomicLibrary-1.1.1.dist-info/WHEEL'
adding 'ChimeraX_AtomicLibrary-1.1.1.dist-info/top_level.txt'
adding 'ChimeraX_AtomicLibrary-1.1.1.dist-info/RECORD'
removing build/bdist.macosx-10.15-x86_64/wheel
Distribution is in ./dist/ChimeraX_AtomicLibrary-1.1.1-cp38-cp38-macosx_10_15_x86_64.whl
Executing: toolshed install ./dist/ChimeraX_AtomicLibrary-1.1.1-cp38-cp38-macosx_10_15_x86_64.whl userOnly false noDeps true
Successfully installed ChimeraX-AtomicLibrary-1.1.1
Installed ChimeraX-AtomicLibrary (1.1.1)

$

[Greg Couch]

Can you reproduce this? This doesn't happen to me on Windows.

Sometimes pip internally calls python (actually sys.executable, which is ChimeraX) to do more work on its behalf. ChimeraX's main program sets the equivalent of the -I command line option to not use the user's environment. So it is good that that argument is passed on to recursive invocations. The question is why.

[goddard@…]

Yes I have seen this warning many times and it happens each time I install atomic_lib on macOS.  Just tried make clean ; make install and get the same -I warning/error messages.

[Greg Couch]

The command line that causes the warning is:

ChimeraX.app/Contents/bin/ChimeraX -I -X faulthandler -c 'from multiprocessing.resource_tracker import main;main(8)'

[Greg Couch]

Changed ChimeraX's sys.argv parsing to recognize all Python options. If the first option starts with a single dash, then the Python options are used. If it starts with a double dash, then the ChimeraX options are used.