Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fail to import pyBBarolo #37

Open
ShanghuoLi opened this issue Jun 23, 2024 · 3 comments
Open

fail to import pyBBarolo #37

ShanghuoLi opened this issue Jun 23, 2024 · 3 comments

Comments

@ShanghuoLi
Copy link

import pyBBarolo

AttributeError Traceback (most recent call last)
Input In [14], in <cell line: 2>()
1 # from pyBBarolo import FitMod3D
----> 2 import pyBBarolo

File ~/anaconda3/lib/python3.9/site-packages/pyBBarolo/init.py:3, in
1 all = ['GalMod','GalWind','FitMod3D','Search','FitMod2D','Ellprof']
----> 3 from .pyBBarolo import *
4 from ._version import version as version

File ~/anaconda3/lib/python3.9/site-packages/pyBBarolo/pyBBarolo.py:25, in
23 import os,sys
24 import numpy as np
---> 25 from .BB_interface import libBB
26 from astropy.io import fits
29 def reshapePointer (p, shape):

File ~/anaconda3/lib/python3.9/site-packages/pyBBarolo/BB_interface.py:43, in
39 array_1d_double = ndpointer(dtype=np.double, ndim=1,flags="CONTIGUOUS")
42 # Class Cube interface #################################################################
---> 43 libBB.Cube_new.restype = c_void_p
44 libBB.Cube_new.argtypes = [c_char_p]
45 libBB.Cube_delete.restype = None

File ~/anaconda3/lib/python3.9/ctypes/init.py:395, in CDLL.getattr(self, name)
393 if name.startswith('') and name.endswith(''):
394 raise AttributeError(name)
--> 395 func = self.getitem(name)
396 setattr(self, name, func)
397 return func

File ~/anaconda3/lib/python3.9/ctypes/init.py:400, in CDLL.getitem(self, name_or_ordinal)
399 def getitem(self, name_or_ordinal):
--> 400 func = self._FuncPtr((name_or_ordinal, self))
401 if not isinstance(name_or_ordinal, int):
402 func.name = name_or_ordinal

AttributeError: dlsym(0x30884a6e0, Cube_new): symbol not found
@editeodoro
Copy link
Owner

Hello, it looks like the library is not correctly compiled. How did you install pyBBarolo?

@ShanghuoLi
Copy link
Author

I just follow the your github.

./configure
make
make install
make pybbinst

Here is all the infomation of the installation.

./confiure
checking build system type... arm-apple-darwin22.6.0
checking whether to compile using MPI... no
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
configure: WARNING: No MPI compiler found, won't use MPI.
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for g++ option to enable C++11 features... (cached) none needed
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking how to run the C preprocessor... gcc -E
checking whether ln -s works... yes
checking for install... install
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for iostream... yes
checking for fstream... yes
checking for _Bool... no
checking for stdbool.h that conforms to C99... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for g++ option to support OpenMP... unsupported
checking for ranlib... ranlib
configure: Using darwin build option
configure: LIBDIRS
checking for /usr/lib... yes
checking for /usr/local/lib... no
checking for /local/lib... no
checking for /opt/local/lib... yes
checking for /opt/homebrew/lib... yes
configure: -- CFITSIO --
checking for /usr/include/fitsio.h... no
checking for /usr/include/cfitsio/fitsio.h... no
checking for /usr/local/include/fitsio.h... no
checking for /usr/local/include/cfitsio/fitsio.h... no
checking for /opt/local/include/fitsio.h... yes
checking for recv in -lsocket... no
checking for ffopen in -lcfitsio... yes
configure: CFITSIO appears to be available.
checking for /usr/lib/libcfitsio.a... no
checking for /usr/lib/cfitsio/libcfitsio.a... no
checking for /usr/local/lib/libcfitsio.a... no
checking for /usr/local/lib/cfitsio/libcfitsio.a... no
checking for /local/lib/libcfitsio.a... no
checking for /local/lib/cfitsio/libcfitsio.a... no
checking for /opt/local/lib/libcfitsio.a... yes
configure: -- FFTW3 --
checking for /usr/include/fftw3.h... no
checking for /usr/local/include/fftw3.h... no
checking for /opt/local/include/fftw3.h... no
checking for /opt/homebrew/include/fftw3.h... yes
checking for fftw_execute in -lfftw3... yes
configure: FFTW3LIB appears to be available.
checking for /usr/lib/libfftw3.a... no
checking for /usr/lib/fftw3/libfftw3.a... no
checking for /usr/lib/fftw3lib/libfftw3.a... no
checking for /usr/local/lib/libfftw3.a... no
checking for /usr/local/lib/fftw3/libfftw3.a... no
checking for /usr/local/lib/fftw3lib/libfftw3.a... no
checking for /local/lib/libfftw3.a... no
checking for /local/lib/fftw3/libfftw3.a... no
checking for /local/lib/fftw3lib/libfftw3.a... no
checking for /opt/local/lib/libfftw3.a... no
checking for /opt/local/lib/fftw3/libfftw3.a... no
checking for /opt/local/lib/fftw3lib/libfftw3.a... no
checking for /opt/homebrew/lib/libfftw3.a... yes
configure: -- WCSLIB --
checking for /usr/include/wcslib/wcs.h... no
checking for /usr/local/include/wcslib/wcs.h... no
checking for /opt/local/include/wcslib/wcs.h... no
checking for /opt/homebrew/include/wcslib/wcs.h... yes
checking for wcss2p in -lwcs... yes
configure: WCSLIB appears to be available.
checking for /usr/lib/libwcs.a... no
checking for /usr/lib/wcs/libwcs.a... no
checking for /usr/lib/wcslib/libwcs.a... no
checking for /usr/local/lib/libwcs.a... no
checking for /usr/local/lib/wcs/libwcs.a... no
checking for /usr/local/lib/wcslib/libwcs.a... no
checking for /local/lib/libwcs.a... no
checking for /local/lib/wcs/libwcs.a... no
checking for /local/lib/wcslib/libwcs.a... no
checking for /opt/local/lib/libwcs.a... no
checking for /opt/local/lib/wcs/libwcs.a... no
checking for /opt/local/lib/wcslib/libwcs.a... no
checking for /opt/homebrew/lib/libwcs.a... yes
configure: -- PYTHON --
checking for python... /Users/li/anaconda3/bin/python
checking for python version... 3.9
checking for python platform... darwin
checking for python script directory... ${prefix}/lib/python3.9/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python3.9/site-packages
checking for python3.9-config... /Users/li/anaconda3/bin/python3.9-config
checking python include flags... -I/Users/li/anaconda3/include/python3.9 -I/Users/li/anaconda3/include/python3.9
checking python lib flags... -L/Users/li/anaconda3/lib/python3.9/config-3.9-darwin -ldl -framework CoreFoundation
checking for module matplotlib in python... yes
checking for module astropy in python... yes
configure: -- GNUPLOT --
checking for gnuplot... yes
configure: creating ./config.status
config.status: creating Makefile
configure:

Configuration Summary:
Operating System: darwin22.6.0
Compiler: g++
Source directory: /Applications/Bbarolo/src
Target directory: /usr/local
CFITSIO library: -L/opt/local/lib -lcfitsio
CFITSIO headers: -I/opt/local/include
FFTW3 library: -L/opt/homebrew/lib -lfftw3
FFTW3 headers: -I/opt/homebrew/include
WCS library: -L/opt/homebrew/lib -lwcs
WCS headers: -I/opt/homebrew/include
Have Gnuplot: -DHAVE_GNUPLOT
Have Python: -DHAVE_PYTHON

configure:

CONGRATULATIONS!

It seems your computer has the needed to compile BBarolo!
Now type "make" and pray to your favoured God.

make
mkdir -p /Applications/Bbarolo/src/Build
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/BB_interface.cpp -o /Applications/Bbarolo/src/Build/BB_interface.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Arrays/cube.cpp -o /Applications/Bbarolo/src/Build/cube.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Arrays/header.cpp -o /Applications/Bbarolo/src/Build/header.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Arrays/image.cpp -o /Applications/Bbarolo/src/Build/image.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Arrays/param.cpp -o /Applications/Bbarolo/src/Build/param.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Arrays/stats.cpp -o /Applications/Bbarolo/src/Build/stats.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Map/detection.cpp -o /Applications/Bbarolo/src/Build/detection.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Map/object2D.cpp -o /Applications/Bbarolo/src/Build/object2D.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Map/object3D.cpp -o /Applications/Bbarolo/src/Build/object3D.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Map/objectgrower.cpp -o /Applications/Bbarolo/src/Build/objectgrower.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Map/scan.cpp -o /Applications/Bbarolo/src/Build/scan.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Map/voxel.cpp -o /Applications/Bbarolo/src/Build/voxel.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/conv2D.cpp -o /Applications/Bbarolo/src/Build/conv2D.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/converter.cpp -o /Applications/Bbarolo/src/Build/converter.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/fitsUtils.cpp -o /Applications/Bbarolo/src/Build/fitsUtils.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/interpolation.cpp -o /Applications/Bbarolo/src/Build/interpolation.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/lsqfit.cpp -o /Applications/Bbarolo/src/Build/lsqfit.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/paramguess.cpp -o /Applications/Bbarolo/src/Build/paramguess.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/progressbar.cpp -o /Applications/Bbarolo/src/Build/progressbar.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/statistics.cpp -o /Applications/Bbarolo/src/Build/statistics.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/string.cpp -o /Applications/Bbarolo/src/Build/string.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/utils.cpp -o /Applications/Bbarolo/src/Build/utils.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Utilities/wcsUtils.cpp -o /Applications/Bbarolo/src/Build/wcsUtils.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/ellprof.cpp -o /Applications/Bbarolo/src/Build/ellprof.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/galfit.cpp -o /Applications/Bbarolo/src/Build/galfit.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/galfit_errors.cpp -o /Applications/Bbarolo/src/Build/galfit_errors.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/galfit_min.cpp -o /Applications/Bbarolo/src/Build/galfit_min.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/galfit_out.cpp -o /Applications/Bbarolo/src/Build/galfit_out.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/galmod.cpp -o /Applications/Bbarolo/src/Build/galmod.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/galwind.cpp -o /Applications/Bbarolo/src/Build/galwind.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/moment.cpp -o /Applications/Bbarolo/src/Build/moment.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/ringmodel.cpp -o /Applications/Bbarolo/src/Build/ringmodel.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/search.cpp -o /Applications/Bbarolo/src/Build/search.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/slitfit.cpp -o /Applications/Bbarolo/src/Build/slitfit.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/smooth3D.cpp -o /Applications/Bbarolo/src/Build/smooth3D.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS -MMD -c /Applications/Bbarolo/src/Tasks/spacepar.cpp -o /Applications/Bbarolo/src/Build/spacepar.o -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -flto -o BBarolo -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include /Applications/Bbarolo/src/bbarolo.cpp /Applications/Bbarolo/src/Build/BB_interface.o /Applications/Bbarolo/src/Build/cube.o /Applications/Bbarolo/src/Build/header.o /Applications/Bbarolo/src/Build/image.o /Applications/Bbarolo/src/Build/param.o /Applications/Bbarolo/src/Build/stats.o /Applications/Bbarolo/src/Build/detection.o /Applications/Bbarolo/src/Build/object2D.o /Applications/Bbarolo/src/Build/object3D.o /Applications/Bbarolo/src/Build/objectgrower.o /Applications/Bbarolo/src/Build/scan.o /Applications/Bbarolo/src/Build/voxel.o /Applications/Bbarolo/src/Build/conv2D.o /Applications/Bbarolo/src/Build/converter.o /Applications/Bbarolo/src/Build/fitsUtils.o /Applications/Bbarolo/src/Build/interpolation.o /Applications/Bbarolo/src/Build/lsqfit.o /Applications/Bbarolo/src/Build/paramguess.o /Applications/Bbarolo/src/Build/progressbar.o /Applications/Bbarolo/src/Build/statistics.o /Applications/Bbarolo/src/Build/string.o /Applications/Bbarolo/src/Build/utils.o /Applications/Bbarolo/src/Build/wcsUtils.o /Applications/Bbarolo/src/Build/ellprof.o /Applications/Bbarolo/src/Build/galfit.o /Applications/Bbarolo/src/Build/galfit_errors.o /Applications/Bbarolo/src/Build/galfit_min.o /Applications/Bbarolo/src/Build/galfit_out.o /Applications/Bbarolo/src/Build/galmod.o /Applications/Bbarolo/src/Build/galwind.o /Applications/Bbarolo/src/Build/moment.o /Applications/Bbarolo/src/Build/ringmodel.o /Applications/Bbarolo/src/Build/search.o /Applications/Bbarolo/src/Build/slitfit.o /Applications/Bbarolo/src/Build/smooth3D.o /Applications/Bbarolo/src/Build/spacepar.o -L/opt/homebrew/lib -lfftw3 -L/opt/local/lib -lcfitsio -L/opt/homebrew/lib -lwcs -lm -DHAVE_GNUPLOT -DHAVE_FFTW3 -DHAVE_PYTHON -DMACOS

sudo make install
install -d -m 2755 /usr/local/bin
cp BBarolo BBarolo-1.7
rm -f /usr/local/bin/BBarolo /usr/local/bin/BBarolo-1.7
install -m 755 BBarolo-1.7 /usr/local/bin
ln -s /usr/local/bin/BBarolo-1.7 /usr/local/bin/BBarolo
rm -f BBarolo-1.7

make pybbinst
ar cq libBBarolo-1.7.a /Applications/Bbarolo/src/Build/BB_interface.o /Applications/Bbarolo/src/Build/cube.o /Applications/Bbarolo/src/Build/header.o /Applications/Bbarolo/src/Build/image.o /Applications/Bbarolo/src/Build/param.o /Applications/Bbarolo/src/Build/stats.o /Applications/Bbarolo/src/Build/detection.o /Applications/Bbarolo/src/Build/object2D.o /Applications/Bbarolo/src/Build/object3D.o /Applications/Bbarolo/src/Build/objectgrower.o /Applications/Bbarolo/src/Build/scan.o /Applications/Bbarolo/src/Build/voxel.o /Applications/Bbarolo/src/Build/conv2D.o /Applications/Bbarolo/src/Build/converter.o /Applications/Bbarolo/src/Build/fitsUtils.o /Applications/Bbarolo/src/Build/interpolation.o /Applications/Bbarolo/src/Build/lsqfit.o /Applications/Bbarolo/src/Build/paramguess.o /Applications/Bbarolo/src/Build/progressbar.o /Applications/Bbarolo/src/Build/statistics.o /Applications/Bbarolo/src/Build/string.o /Applications/Bbarolo/src/Build/utils.o /Applications/Bbarolo/src/Build/wcsUtils.o /Applications/Bbarolo/src/Build/ellprof.o /Applications/Bbarolo/src/Build/galfit.o /Applications/Bbarolo/src/Build/galfit_errors.o /Applications/Bbarolo/src/Build/galfit_min.o /Applications/Bbarolo/src/Build/galfit_out.o /Applications/Bbarolo/src/Build/galmod.o /Applications/Bbarolo/src/Build/galwind.o /Applications/Bbarolo/src/Build/moment.o /Applications/Bbarolo/src/Build/ringmodel.o /Applications/Bbarolo/src/Build/search.o /Applications/Bbarolo/src/Build/slitfit.o /Applications/Bbarolo/src/Build/smooth3D.o /Applications/Bbarolo/src/Build/spacepar.o
ranlib libBBarolo-1.7.a
g++ -O2 -ftree-vectorize -fPIC -Wuninitialized -std=c++17 -flto -fPIC -dynamiclib -single_module -compatibility_version 1.7 -current_version 1.7 -I/Applications/Bbarolo/src -I/opt/homebrew/include -I/opt/local/include -I/opt/homebrew/include -L/opt/homebrew/lib -lfftw3 -L/opt/local/lib -lcfitsio -L/opt/homebrew/lib -lwcs -lm -o libBBarolo.dylib.1.7 /Applications/Bbarolo/src/Build/BB_interface.o /Applications/Bbarolo/src/Build/cube.o /Applications/Bbarolo/src/Build/header.o /Applications/Bbarolo/src/Build/image.o /Applications/Bbarolo/src/Build/param.o /Applications/Bbarolo/src/Build/stats.o /Applications/Bbarolo/src/Build/detection.o /Applications/Bbarolo/src/Build/object2D.o /Applications/Bbarolo/src/Build/object3D.o /Applications/Bbarolo/src/Build/objectgrower.o /Applications/Bbarolo/src/Build/scan.o /Applications/Bbarolo/src/Build/voxel.o /Applications/Bbarolo/src/Build/conv2D.o /Applications/Bbarolo/src/Build/converter.o /Applications/Bbarolo/src/Build/fitsUtils.o /Applications/Bbarolo/src/Build/interpolation.o /Applications/Bbarolo/src/Build/lsqfit.o /Applications/Bbarolo/src/Build/paramguess.o /Applications/Bbarolo/src/Build/progressbar.o /Applications/Bbarolo/src/Build/statistics.o /Applications/Bbarolo/src/Build/string.o /Applications/Bbarolo/src/Build/utils.o /Applications/Bbarolo/src/Build/wcsUtils.o /Applications/Bbarolo/src/Build/ellprof.o /Applications/Bbarolo/src/Build/galfit.o /Applications/Bbarolo/src/Build/galfit_errors.o /Applications/Bbarolo/src/Build/galfit_min.o /Applications/Bbarolo/src/Build/galfit_out.o /Applications/Bbarolo/src/Build/galmod.o /Applications/Bbarolo/src/Build/galwind.o /Applications/Bbarolo/src/Build/moment.o /Applications/Bbarolo/src/Build/ringmodel.o /Applications/Bbarolo/src/Build/search.o /Applications/Bbarolo/src/Build/slitfit.o /Applications/Bbarolo/src/Build/smooth3D.o /Applications/Bbarolo/src/Build/spacepar.o
rm -rf libBBarolo.dylib libBBarolo.a
ln -s libBBarolo.dylib.1.7 libBBarolo.dylib
ln -s libBBarolo-1.7.a libBBarolo.a
mv libBBarolo-1.7.a /Applications/Bbarolo/src/../pyBBarolo
mv libBBarolo.a /Applications/Bbarolo/src/../pyBBarolo
mv libBBarolo.dylib.1.7 /Applications/Bbarolo/src/../pyBBarolo
mv libBBarolo.dylib /Applications/Bbarolo/src/../pyBBarolo
pip install .
Processing /Applications/Bbarolo
Preparing metadata (setup.py) ... done
Building wheels for collected packages: pyBBarolo
Building wheel for pyBBarolo (setup.py) ... done
Created wheel for pyBBarolo: filename=pyBBarolo-1.3.1-py3-none-any.whl size=3513202 sha256=e2f74d768c20a77a713d3c7a8001ea87e88de28cf13c5e333d74aa5283302c76
Stored in directory: /private/var/folders/s_/m2r__lf92jz8jls49m8fqhdn5_hb19/T/pip-ephem-wheel-cache-5z740c1f/wheels/34/67/eb/beb63a83dcb2cd0d4d5b67b6a3cde3fadd96e26efdce7dca65
Successfully built pyBBarolo
Installing collected packages: pyBBarolo
Attempting uninstall: pyBBarolo
Found existing installation: pyBBarolo 1.3.1
Uninstalling pyBBarolo-1.3.1:
Successfully uninstalled pyBBarolo-1.3.1
Successfully installed pyBBarolo-1.3.1
rm -rf build dist MANIFEST
rm -rf pyBBarolo/BBarolo pyBBarolo/libBB*

@editeodoro
Copy link
Owner

Sorry, I can not reproduce this error on my machines, so it is difficult to figure out what's happening. It could be that the code is being compiled with the default CLANG on your Mac? The latest versions of this compiler seem to fail in compiling the code correctly. Could you try to recompile the code using the GNU-g++?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@editeodoro @ShanghuoLi