treverhines
commented
6 years ago did you try running xcode-select --install as described here https://stackoverflow.com/questions/30877659/fatal-error-limits-h-no-such-file-or-directory ?
Closed logan-nc closed 6 years ago
treverhines
commented
6 years ago did you try running xcode-select --install as described here https://stackoverflow.com/questions/30877659/fatal-error-limits-h-no-such-file-or-directory ?
logan-nc
commented
6 years ago Thanks. That got it to run through, but with the following warnings
nlogan-lt1:RBF nlogan$ python setup.py install
running install
running bdist_egg
running egg_info
writing RBF.egg-info/PKG-INFO
writing top-level names to RBF.egg-info/top_level.txt
writing dependency_links to RBF.egg-info/dependency_links.txt
reading manifest file 'RBF.egg-info/SOURCES.txt'
writing manifest file 'RBF.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.9-x86_64/egg
running install_lib
running build_py
running build_ext
building 'rbf.halton' extension
gcc -fno-strict-aliasing -I/Users/nlogan/Code/miniconda2/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/nlogan/Code/miniconda2/include/python2.7 -c rbf/halton.c -o build/temp.macosx-10.9-x86_64-2.7/rbf/halton.o
In file included from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0,
from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from rbf/halton.c:586:
/Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
gcc -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/nlogan/Code/miniconda2/lib -L/Users/nlogan/Code/miniconda2/lib -headerpad_max_install_names -arch x86_64 build/temp.macosx-10.9-x86_64-2.7/rbf/halton.o -L/Users/nlogan/Code/miniconda2/lib -o build/lib.macosx-10.9-x86_64-2.7/rbf/halton.so
building 'rbf.misc.bspline' extension
creating build/temp.macosx-10.9-x86_64-2.7/rbf/misc
gcc -fno-strict-aliasing -I/Users/nlogan/Code/miniconda2/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/nlogan/Code/miniconda2/include/python2.7 -c rbf/misc/bspline.c -o build/temp.macosx-10.9-x86_64-2.7/rbf/misc/bspline.o
In file included from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0,
from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from rbf/misc/bspline.c:586:
/Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
gcc -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/nlogan/Code/miniconda2/lib -L/Users/nlogan/Code/miniconda2/lib -headerpad_max_install_names -arch x86_64 build/temp.macosx-10.9-x86_64-2.7/rbf/misc/bspline.o -L/Users/nlogan/Code/miniconda2/lib -o build/lib.macosx-10.9-x86_64-2.7/rbf/misc/bspline.so
building 'rbf.geometry' extension
gcc -fno-strict-aliasing -I/Users/nlogan/Code/miniconda2/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/nlogan/Code/miniconda2/include/python2.7 -c rbf/geometry.c -o build/temp.macosx-10.9-x86_64-2.7/rbf/geometry.o
In file included from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0,
from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from rbf/geometry.c:586:
/Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
rbf/geometry.c:2832:49: warning: ‘__pyx_f_3rbf_8geometry_allocate_segment2d_array’ defined but not used [-Wunused-function]
static struct __pyx_t_3rbf_8geometry_segment2d *__pyx_f_3rbf_8geometry_allocate_segment2d_array(long __pyx_v_n) {
^
rbf/geometry.c:2911:49: warning: ‘__pyx_f_3rbf_8geometry_allocate_segment3d_array’ defined but not used [-Wunused-function]
static struct __pyx_t_3rbf_8geometry_segment3d *__pyx_f_3rbf_8geometry_allocate_segment3d_array(long __pyx_v_n) {
^
gcc -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/nlogan/Code/miniconda2/lib -L/Users/nlogan/Code/miniconda2/lib -headerpad_max_install_names -arch x86_64 build/temp.macosx-10.9-x86_64-2.7/rbf/geometry.o -L/Users/nlogan/Code/miniconda2/lib -o build/lib.macosx-10.9-x86_64-2.7/rbf/geometry.so
building 'rbf.poly' extension
gcc -fno-strict-aliasing -I/Users/nlogan/Code/miniconda2/include -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include -I/Users/nlogan/Code/miniconda2/include/python2.7 -c rbf/poly.c -o build/temp.macosx-10.9-x86_64-2.7/rbf/poly.o
In file included from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1816:0,
from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from rbf/poly.c:586:
/Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
gcc -bundle -undefined dynamic_lookup -Wl,-rpath,/Users/nlogan/Code/miniconda2/lib -L/Users/nlogan/Code/miniconda2/lib -headerpad_max_install_names -arch x86_64 build/temp.macosx-10.9-x86_64-2.7/rbf/poly.o -L/Users/nlogan/Code/miniconda2/lib -o build/lib.macosx-10.9-x86_64-2.7/rbf/poly.so
creating build/bdist.macosx-10.9-x86_64
creating build/bdist.macosx-10.9-x86_64/egg
creating build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/basis.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/domain.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/fd.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/fdbuild.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/gauss.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/geometry.so -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/halton.so -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/interpolate.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/linalg.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
creating build/bdist.macosx-10.9-x86_64/egg/rbf/misc
copying build/lib.macosx-10.9-x86_64-2.7/rbf/misc/__init__.py -> build/bdist.macosx-10.9-x86_64/egg/rbf/misc
copying build/lib.macosx-10.9-x86_64-2.7/rbf/misc/bspline.so -> build/bdist.macosx-10.9-x86_64/egg/rbf/misc
copying build/lib.macosx-10.9-x86_64-2.7/rbf/misc/filter.py -> build/bdist.macosx-10.9-x86_64/egg/rbf/misc
copying build/lib.macosx-10.9-x86_64-2.7/rbf/misc/formulation.py -> build/bdist.macosx-10.9-x86_64/egg/rbf/misc
copying build/lib.macosx-10.9-x86_64-2.7/rbf/misc/integrate.py -> build/bdist.macosx-10.9-x86_64/egg/rbf/misc
copying build/lib.macosx-10.9-x86_64-2.7/rbf/mp.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/nodes.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/poly.so -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/stencil.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
copying build/lib.macosx-10.9-x86_64-2.7/rbf/utils.py -> build/bdist.macosx-10.9-x86_64/egg/rbf
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/basis.py to basis.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/domain.py to domain.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/fd.py to fd.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/fdbuild.py to fdbuild.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/gauss.py to gauss.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/interpolate.py to interpolate.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/linalg.py to linalg.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/misc/__init__.py to __init__.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/misc/filter.py to filter.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/misc/formulation.py to formulation.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/misc/integrate.py to integrate.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/mp.py to mp.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/nodes.py to nodes.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/stencil.py to stencil.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/utils.py to utils.pyc
creating stub loader for rbf/halton.so
creating stub loader for rbf/misc/bspline.so
creating stub loader for rbf/geometry.so
creating stub loader for rbf/poly.so
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/halton.py to halton.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/misc/bspline.py to bspline.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/geometry.py to geometry.pyc
byte-compiling build/bdist.macosx-10.9-x86_64/egg/rbf/poly.py to poly.pyc
creating build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying RBF.egg-info/PKG-INFO -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying RBF.egg-info/SOURCES.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying RBF.egg-info/dependency_links.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
copying RBF.egg-info/top_level.txt -> build/bdist.macosx-10.9-x86_64/egg/EGG-INFO
writing build/bdist.macosx-10.9-x86_64/egg/EGG-INFO/native_libs.txt
zip_safe flag not set; analyzing archive contents...
creating dist
creating 'dist/RBF-2018.7.15-py2.7-macosx-10.9-x86_64.egg' and adding 'build/bdist.macosx-10.9-x86_64/egg' to it
removing 'build/bdist.macosx-10.9-x86_64/egg' (and everything under it)
Processing RBF-2018.7.15-py2.7-macosx-10.9-x86_64.egg
Copying RBF-2018.7.15-py2.7-macosx-10.9-x86_64.egg to /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages
Adding RBF 2018.7.15 to easy-install.pth file
Installed /Users/nlogan/Code/miniconda2/lib/python2.7/site-packages/RBF-2018.7.15-py2.7-macosx-10.9-x86_64.egg
Processing dependencies for RBF==2018.7.15
Finished processing dependencies for RBF==2018.7.15This seems close, but I was not able to import
In [1]: import rbf
?[0;31m---------------------------------------------------------------------------?[0m
?[0;31mImportError?[0m Traceback (most recent call last)
?[0;32m<ipython-input-1-e3dd23f063ee>?[0m in ?[0;36m<module>?[0;34m()?[0m
?[0;32m----> 1?[0;31m ?[0;32mimport?[0m ?[0mrbf?[0m?[0;34m?[0m?[0m
?[0m
?[0;32mbuild/bdist.macosx-10.9-x86_64/egg/rbf/__init__.py?[0m in ?[0;36m<module>?[0;34m()?[0m
?[0;32mbuild/bdist.macosx-10.9-x86_64/egg/rbf/basis.py?[0m in ?[0;36m<module>?[0;34m()?[0m
?[0;31mImportError?[0m: No module named sympyor put another way,
In [2]: %run ~/Downloads/gauss.j.py
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
/Users/nlogan/Downloads/gauss.j.py in <module>()
5 import matplotlib.pyplot as plt
6 import numpy as np
----> 7 import rbf
8 from rbf.gauss import gpiso,gppoly
9
build/bdist.macosx-10.9-x86_64/egg/rbf/__init__.py in <module>()
build/bdist.macosx-10.9-x86_64/egg/rbf/basis.py in <module>()
ImportError: No module named sympyGreat! The remaining dependencies can be satisfied with conda. So run 'conda install sympy' and 'conda install networkx'. You will also get a notification about not having CHOLMOD. You do want this package because it is for interpolating with sparse kernels. Install it with 'conda install -c conda-forge scikit-sparse'
logan-nc
commented
6 years ago Done! Everything works beautifully.
Hi @treverhines. I'm excited to try out your RBF package, but am having trouble with the install step.
The error:
Background: I use conda, and got gcc through conda after an initial fail using whatever other gcc I had before (same error). My conda list is:
Let me know if there is some dependency I am not satisfying.