Open ghost opened 3 years ago
Hey. I'm having the same problem, did you manage to fix it?
I have the exact same problem!
The original issue report uses PyBDSF 1.9.1, which is quite old. The latest release is 1.10.1 (https://github.com/lofar-astron/PyBDSF/archive/refs/tags/v1.10.1.tar.gz). Do you have the same issue with that release? I don't have a Mac at hand, so I cannot investigate the problem myself. But I would like to know if the problem persists in the latest release.
Hi gmloose,
I have just tried to install the latest version using pip and I am still getting the same error - Please see attached
OK, could you please attach the complete log file of the build. I.e. just redirect all output to a file and upload that to GitHub.
Please see attached text file
You're not facing the same problem. At least, I cannot tell yet. It seems you don't have the boost libraries installed on your machine, at least not boost_numpy
, since that's what the build is complaining about.
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
setup.py:161: UserWarning:
Could not find a Python boost library! Please use your package manager to install boost.
Or install it manually:
http://boostorg.github.io/python/doc/html/index.html
warnings.warn(no_boost_error)
setup.py:194: UserWarning: No library boost_numpy found (this may be no problem)
warnings.warn("No library boost_numpy found (this may be no problem)")
You could try to run pip install
with the --no-clean
option, and then try to execute the failing command (gfortran -fPIC -c lmder.f
) manually, in the temporary build directory. This may provide more background to the actual problem.
Could you also please indicate which version of pip
, setuptools
, and wheel
you're using?
pip list | egrep 'pip|setuptools|wheel'
In response to: pip list | egrep 'pip|setuptools|wheel' pip 21.0.1 setuptools 52.0.0.post20210125 wheel 0.36.2
pip 21.0.1 setuptools 52.0.0.post20210125 wheel 0.36.2
Those should be recent enough. Did you already try to install the Boost Numpy libraries and headers? On my Linux machine, I have no issues using Boost 1.71, but on MacOS things could obviously be different :)
Please note the text: "No library boost_numpy found (this may be no problem)"
. On some versions of boost, the numpy module is part of boost-python
. I have not checked whether this is the case on macos.
Tried to install with "pip install https://github.com/lofar-astron/PyBDSF/archive/v1.9.1.tar.gz"
Collecting https://github.com/lofar-astron/PyBDSF/archive/v1.9.1.tar.gz WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='github.com', port=443): Read timed out. (read timeout=15)")': /lofar-astron/PyBDSF/archive/v1.9.1.tar.gz WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='github.com', port=443): Read timed out. (read timeout=15)")': /lofar-astron/PyBDSF/archive/v1.9.1.tar.gz Using cached https://github.com/lofar-astron/PyBDSF/archive/v1.9.1.tar.gz Requirement already satisfied: backports.shutil_get_terminal_size in ./opt/anaconda3/lib/python3.8/site-packages (from bdsf==1.9.1) (1.0.0) Requirement already satisfied: numpy in ./opt/anaconda3/lib/python3.8/site-packages (from bdsf==1.9.1) (1.19.1) Requirement already satisfied: scipy in ./opt/anaconda3/lib/python3.8/site-packages (from bdsf==1.9.1) (1.5.0) Building wheels for collected packages: bdsf Building wheel for bdsf (setup.py) ... error ERROR: Command errored out with exit status 1: command: /Users/chenzhengyi/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-req-build-485n7cht/setup.py'"'"'; file='"'"'/private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-req-build-485n7cht/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-wheel-57ec4spj cwd: /private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-req-build-485n7cht/ Complete output (277 lines): running bdist_wheel running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "bdsf._pytesselate" sources f2py options: [''] adding 'build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/fortranobject.c' to sources. adding 'build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf' to include_dirs. building extension "bdsf._cbdsm" sources building extension "bdsf.nat.natgridmodule" sources build_src: building npy-pkg config files running build_py creating build/lib.macosx-10.9-x86_64-3.8 creating build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/wavelet_atrous.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/functions.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/mylogger.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/tc.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/statusbar.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/islands.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/sourcecounts.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/_version.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/preprocess.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/multi_proc.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/psf_vary.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/gaul2srl.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/readimage.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/interface.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/collapse.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/init.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/shapelets.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/cleanup.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/threshold.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/spectralindex.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/make_residimage.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/opts.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/polarisation.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/rmsimage.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/gausfit.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/shapefit.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/plotresults.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/image.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/const.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/output.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf creating build/lib.macosx-10.9-x86_64-3.8/bdsf/nat copying bdsf/nat/init.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf/nat running build_ext running mbuild Building libminpack Building libport3 dnsg.f:308:72:
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) dn2g.f:176:72:
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) drnsg.f:219:72:
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) drnsg.f:290:72:
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 130 at (1) drn2g.f:264:72:
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) dd7upd.f:58:72:
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1) dg7qts.f:282:72:
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Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2) dg7qts.f:368:22:
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2) ditsum.f:243:72:
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Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) dn2rdp.f:31:72:
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1) ds7lup.f:42:72:
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Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1) customize UnixCCompiler customize UnixCCompiler using BuildExt customize UnixCCompiler customize UnixCCompiler using BuildExt get_default_fcompiler: matching types: '['gnu95', 'nag', 'absoft', 'ibm', 'intel', 'gnu', 'g95', 'pg']' customize Gnu95FCompiler Found executable /usr/local/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using BuildExt building 'bdsf._pytesselate' extension compiling C sources C compiler: gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/chenzhengyi/opt/anaconda3/include -arch x86_64 -I/Users/chenzhengyi/opt/anaconda3/include -arch x86_64
creating build/temp.macosx-10.9-x86_64-3.8/build creating build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8 creating build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf creating build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/build creating build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8 creating build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf compile options: '-Ibuild/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf -I/Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/chenzhengyi/opt/anaconda3/include/python3.8 -c' gcc: build/src.macosx-10.9-x86_64-3.8/bdsf/_pytesselatemodule.c gcc: build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/fortranobject.c In file included from build/src.macosx-10.9-x86_64-3.8/bdsf/_pytesselatemodule.c:16: In file included from build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/fortranobject.h:13: In file included from /Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
warning "Using deprecated NumPy API, disable it with " \
^ In file included from build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/fortranobject.c:2: In file included from build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/fortranobject.h:13: In file included from /Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/arrayobject.h:4: In file included from /Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarrayobject.h:12: In file included from /Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822: /Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
warning "Using deprecated NumPy API, disable it with " \
^ build/src.macosx-10.9-x86_64-3.8/bdsf/_pytesselatemodule.c:142:12: warning: unused function 'f2py_size' [-Wunused-function] static int f2py_size(PyArrayObject* var, ...) ^ 2 warnings generated. 1 warning generated. compiling Fortran sources Fortran f77 compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/local/bin/gfortran -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/local/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -arch x86_64 -fPIC -O3 -funroll-loops creating build/temp.macosx-10.9-x86_64-3.8/src creating build/temp.macosx-10.9-x86_64-3.8/src/fortran compile options: '-Ibuild/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf -I/Users/chenzhengyi/opt/anaconda3/lib/python3.8/site-packages/numpy/core/include -I/Users/chenzhengyi/opt/anaconda3/include/python3.8 -c' gfortran:f77: src/fortran/pytess_simple.f gfortran:f77: src/fortran/pytess_roundness.f src/fortran/pytess_roundness.f:30:24:
Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1) [-Wconversion] /usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/_pytesselatemodule.o build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/fortranobject.o build/temp.macosx-10.9-x86_64-3.8/src/fortran/pytess_simple.o build/temp.macosx-10.9-x86_64-3.8/src/fortran/pytess_roundness.o -L/usr/local/Cellar/gcc/10.2.0_2/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_2/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0/../../.. -L/usr/local/Cellar/gcc/10.2.0_2/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0/../../.. -lgfortran -o build/lib.macosx-10.9-x86_64-3.8/bdsf/_pytesselate.cpython-38-darwin.so ld: unexpected token: !tapi-tbd-v3 file '/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/lib/libSystem.tbd' for architecture x86_64 collect2: fatal error: ld terminated with signal 11 [Segmentation fault: 11] compilation terminated. error: Command "/usr/local/bin/gfortran -Wall -g -arch x86_64 -Wall -g -undefined dynamic_lookup -bundle build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/_pytesselatemodule.o build/temp.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/fortranobject.o build/temp.macosx-10.9-x86_64-3.8/src/fortran/pytess_simple.o build/temp.macosx-10.9-x86_64-3.8/src/fortran/pytess_roundness.o -L/usr/local/Cellar/gcc/10.2.0_2/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0 -L/usr/local/Cellar/gcc/10.2.0_2/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0/../../.. -L/usr/local/Cellar/gcc/10.2.0_2/lib/gcc/10/gcc/x86_64-apple-darwin19/10.2.0/../../.. -lgfortran -o build/lib.macosx-10.9-x86_64-3.8/bdsf/_pytesselate.cpython-38-darwin.so" failed with exit status 1
ERROR: Failed building wheel for bdsf Running setup.py clean for bdsf Failed to build bdsf Installing collected packages: bdsf Running setup.py install for bdsf ... error ERROR: Command errored out with exit status 1: command: /Users/chenzhengyi/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-req-build-485n7cht/setup.py'"'"'; file='"'"'/private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-req-build-485n7cht/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-record-7kpg2b87/install-record.txt --single-version-externally-managed --compile --install-headers /Users/chenzhengyi/opt/anaconda3/include/python3.8/bdsf cwd: /private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-req-build-485n7cht/ Complete output (276 lines): running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "bdsf._pytesselate" sources f2py options: [''] adding 'build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf/fortranobject.c' to sources. adding 'build/src.macosx-10.9-x86_64-3.8/build/src.macosx-10.9-x86_64-3.8/bdsf' to include_dirs. building extension "bdsf._cbdsm" sources building extension "bdsf.nat.natgridmodule" sources build_src: building npy-pkg config files running build_py creating build/lib.macosx-10.9-x86_64-3.8 creating build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/wavelet_atrous.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/functions.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/mylogger.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/tc.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/statusbar.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/islands.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/sourcecounts.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/_version.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/preprocess.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/multi_proc.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/psf_vary.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/gaul2srl.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/readimage.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/interface.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/collapse.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/init.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/shapelets.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/cleanup.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/threshold.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/spectralindex.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/make_residimage.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/opts.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/polarisation.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/rmsimage.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/gausfit.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/shapefit.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/plotresults.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/image.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/const.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf copying bdsf/output.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf creating build/lib.macosx-10.9-x86_64-3.8/bdsf/nat copying bdsf/nat/init.py -> build/lib.macosx-10.9-x86_64-3.8/bdsf/nat running build_ext running mbuild Building libminpack Building libport3 dnsg.f:308:72:
ERROR: Command errored out with exit status 1: /Users/chenzhengyi/opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-req-build-485n7cht/setup.py'"'"'; file='"'"'/private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-req-build-485n7cht/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /private/var/folders/4h/pj0bjkv50s55t3_6swzc0csm0000gn/T/pip-record-7kpg2b87/install-record.txt --single-version-externally-managed --compile --install-headers /Users/chenzhengyi/opt/anaconda3/include/python3.8/bdsf Check the logs for full command output.