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Cannot install in macOS Big Sur #153

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ghost opened this issue Mar 21, 2021 · 11 comments
Open

Cannot install in macOS Big Sur #153

ghost opened this issue Mar 21, 2021 · 11 comments

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@ghost
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ghost commented Mar 21, 2021 •
edited by ghost
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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:

308 |       IF (IV(1)-2) 110, 120, 999
    |                                                                        1

Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dn2g.f:176:72:

176 |       IF (IV(1)-2) 30, 50, 60
    |                                                                        1

Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
drnsg.f:219:72:

219 |       IF (IV1-2) 40, 150, 230
    |                                                                        1

Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
drnsg.f:290:72:

290 |  130     CALL DV2AXY(N, V(R1), -C(I), A(1,I), V(R1))
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 130 at (1)
drn2g.f:264:72:

264 |       IF (IV(1) - 2) 50, 60, 220
    |                                                                        1

Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dd7upd.f:58:72:

 58 |  20           T = DMAX1(T, DABS(DR(K,I)))
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)
dg7qts.f:282:72:

282 |  40           W(I) = ZERO
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 40 at (1)
dg7qts.f:436:72:

436 |  230     W(I) = ZERO
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 230 at (1)
dg7qts.f:566:72:

566 |  350     W(I) = T*W(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 350 at (1)
dg7qts.f:571:72:

571 |  360     W(I) = T2*W(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 360 at (1)
dg7qts.f:331:22:

329 |       DO 110 I = 2, P
    |                                                                        2
330 |          J = DIAG0 + I
331 |          T = W(J) - W(I)
    |                      1

Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
dg7qts.f:368:22:

366 |       DO 160 I = 2, P
    |                                                                        2
367 |          J = DIAG0 + I
368 |          T = W(J) + W(I)
    |                      1

Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
ditsum.f:243:72:

243 |  480          WRITE(PU,490) I, X(I), D(I), G(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 480 at (1)
dl7itv.f:18:72:

 18 |  10      X(I) = Y(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
dl7mst.f:211:72:

211 |       IF (KA) 10, 20, 370
    |                                                                        1

Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dl7mst.f:262:72:

262 |  100     W(I) = G(I)/D(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 100 at (1)
dl7mst.f:287:72:

287 |  120     W(I) = ONE
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 120 at (1)
dl7mst.f:391:72:

391 |  250                    STEP(K) = STEP(K)/DFAC
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 250 at (1)
dl7mst.f:433:72:

433 |  340     STEP(I) = STEP(I) / DSQRT(W(I))
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 340 at (1)
dl7mst.f:472:72:

472 |  400     STEP(I) = ZERO
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 400 at (1)
dl7svn.f:156:72:

156 |  70      X(I) = T*X(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 70 at (1)
dl7svx.f:144:72:

144 |  50      X(I) = T*X(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 50 at (1)
dl7tsq.f:31:72:

 31 |  40           A(J) = LII * L(J)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 40 at (1)
dn2cvp.f:55:72:

 55 |       IF (COV1) 80,110,130
    |                                                                        1

Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dn2rdp.f:31:72:

 31 |       IF (V(F)) 10, 30, 10
    |                                                                        1

Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
ds7lup.f:42:72:

 42 |  10      W(I) = T * WCHMTD(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
ds7lup.f:46:72:

 46 |  20      U(I) = T*W(I) + Y(I) - SIZE*U(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)
dv2axy.f:11:72:

 11 |  10      W(I) = A*X(I) + Y(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
dv7cpy.f:11:72:

 11 |  10      Y(I) = X(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
dv7scl.f:11:72:

 11 |  10       X(I) = A * Y(I)
    |                                                                        1

Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
dv7scp.f:11:72:

 11 |  10      Y(I) = S
    |                                                                        1

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:

 30 |          roundfacold(i)=roundfac(i)
    |                        1

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:

  308 |       IF (IV(1)-2) 110, 120, 999
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dn2g.f:176:72:

  176 |       IF (IV(1)-2) 30, 50, 60
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
drnsg.f:219:72:

  219 |       IF (IV1-2) 40, 150, 230
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
drnsg.f:290:72:

  290 |  130     CALL DV2AXY(N, V(R1), -C(I), A(1,I), V(R1))
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 130 at (1)
drn2g.f:264:72:

  264 |       IF (IV(1) - 2) 50, 60, 220
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dd7upd.f:58:72:

   58 |  20           T = DMAX1(T, DABS(DR(K,I)))
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)
dg7qts.f:282:72:

  282 |  40           W(I) = ZERO
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 40 at (1)
dg7qts.f:436:72:

  436 |  230     W(I) = ZERO
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 230 at (1)
dg7qts.f:566:72:

  566 |  350     W(I) = T*W(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 350 at (1)
dg7qts.f:571:72:

  571 |  360     W(I) = T2*W(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 360 at (1)
dg7qts.f:331:22:

  329 |       DO 110 I = 2, P
      |                                                                        2
  330 |          J = DIAG0 + I
  331 |          T = W(J) - W(I)
      |                      1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
dg7qts.f:368:22:

  366 |       DO 160 I = 2, P
      |                                                                        2
  367 |          J = DIAG0 + I
  368 |          T = W(J) + W(I)
      |                      1
Warning: Array reference at (1) out of bounds (2 > 1) in loop beginning at (2)
ditsum.f:243:72:

  243 |  480          WRITE(PU,490) I, X(I), D(I), G(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 480 at (1)
dl7itv.f:18:72:

   18 |  10      X(I) = Y(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
dl7mst.f:211:72:

  211 |       IF (KA) 10, 20, 370
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dl7mst.f:262:72:

  262 |  100     W(I) = G(I)/D(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 100 at (1)
dl7mst.f:287:72:

  287 |  120     W(I) = ONE
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 120 at (1)
dl7mst.f:391:72:

  391 |  250                    STEP(K) = STEP(K)/DFAC
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 250 at (1)
dl7mst.f:433:72:

  433 |  340     STEP(I) = STEP(I) / DSQRT(W(I))
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 340 at (1)
dl7mst.f:472:72:

  472 |  400     STEP(I) = ZERO
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 400 at (1)
dl7svn.f:156:72:

  156 |  70      X(I) = T*X(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 70 at (1)
dl7svx.f:144:72:

  144 |  50      X(I) = T*X(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 50 at (1)
dl7tsq.f:31:72:

   31 |  40           A(J) = LII * L(J)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 40 at (1)
dn2cvp.f:55:72:

   55 |       IF (COV1) 80,110,130
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
dn2rdp.f:31:72:

   31 |       IF (V(F)) 10, 30, 10
      |                                                                        1
Warning: Fortran 2018 deleted feature: Arithmetic IF statement at (1)
ds7lup.f:42:72:

   42 |  10      W(I) = T * WCHMTD(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
ds7lup.f:46:72:

   46 |  20      U(I) = T*W(I) + Y(I) - SIZE*U(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 20 at (1)
dv2axy.f:11:72:

   11 |  10      W(I) = A*X(I) + Y(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
dv7cpy.f:11:72:

   11 |  10      Y(I) = X(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
dv7scl.f:11:72:

   11 |  10       X(I) = A * Y(I)
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 10 at (1)
dv7scp.f:11:72:

   11 |  10      Y(I) = S
      |                                                                        1
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/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 " \
 ^
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 " \
 ^
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:

   30 |          roundfacold(i)=roundfac(i)
      |                        1
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: error: ld returned 1 exit status
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: 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.
@ghost ghost closed this as completed Mar 21, 2021
@ghost ghost reopened this Mar 21, 2021
@IamSphiwe
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Hey. I'm having the same problem, did you manage to fix it?

@ashy2212
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I have the exact same problem!

@gmloose
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gmloose commented Jul 12, 2022

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.

@ashy2212
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Hi gmloose,

I have just tried to install the latest version using pip and I am still getting the same error - Please see attached
Screenshot 2022-07-12 at 10 10 50

Screenshot 2022-07-12 at 10 10 58

@gmloose
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gmloose commented Jul 12, 2022

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.

@ashy2212
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Please see attached text file

PyBDSF.txt

@gmloose
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gmloose commented Jul 12, 2022

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.

@gmloose
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gmloose commented Jul 12, 2022

Could you also please indicate which version of pip, setuptools, and wheel you're using?

pip list | egrep 'pip|setuptools|wheel'

@ashy2212
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In response to: pip list | egrep 'pip|setuptools|wheel'
pip 21.0.1
setuptools 52.0.0.post20210125
wheel 0.36.2

@gmloose
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gmloose commented Jul 12, 2022 •
edited
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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 :)

@tammojan
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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.

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@tammojan @gmloose @IamSphiwe @ashy2212