Installation failed #52
Comments
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After restarting the Mac (and deleting some installed versions of python -- but this is not relevant as I used pyenv instead), I was able to install it successfully. |
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I am now installing the latest version of this package and I am getting the same error. However, restarting does not seem to help this time around. I would appreciate any suggestions. Obtaining file:///Users/igor/Documents/ProjSymbRegTest2/dso |
Dear Petersen,
Thank you very much for this great package. I have tried to install it on a Mac with a clean Python 3.6 in a virtual environment following the instructions but it fails. Here is the error:
(DSO_v2) igor@iMac-SB deep-symbolic-optimization-master % pip install -e ./dso
Obtaining file:///Users/igor/Downloads/deep-symbolic-optimization-master/dso
Preparing metadata (setup.py) ... done
Requirement already satisfied: pytest in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (7.0.1)
Requirement already satisfied: cython in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (0.29.32)
Requirement already satisfied: numpy<=1.19 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (1.19.0)
Requirement already satisfied: tensorflow==1.14 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (1.14.0)
Requirement already satisfied: numba==0.53.1 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (0.53.1)
Requirement already satisfied: sympy in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (1.9)
Requirement already satisfied: pandas in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (1.1.5)
Requirement already satisfied: scikit-learn in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (0.24.2)
Requirement already satisfied: click in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (8.0.4)
Requirement already satisfied: deap in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (1.3.3)
Requirement already satisfied: pathos in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (0.2.8)
Requirement already satisfied: seaborn in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (0.11.2)
Requirement already satisfied: progress in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (1.6)
Requirement already satisfied: tqdm in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (4.64.1)
Requirement already satisfied: commentjson in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (0.9.0)
Requirement already satisfied: PyYAML in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from dso==1.0.dev0) (6.0)
Requirement already satisfied: llvmlite<0.37,>=0.36.0rc1 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from numba==0.53.1->dso==1.0.dev0) (0.36.0)
Requirement already satisfied: setuptools in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from numba==0.53.1->dso==1.0.dev0) (59.6.0)
Requirement already satisfied: keras-preprocessing>=1.0.5 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.1.2)
Requirement already satisfied: six>=1.10.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.16.0)
Requirement already satisfied: wheel>=0.26 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (0.37.1)
Requirement already satisfied: astor>=0.6.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (0.8.1)
Requirement already satisfied: absl-py>=0.7.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.3.0)
Requirement already satisfied: google-pasta>=0.1.6 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (0.2.0)
Requirement already satisfied: wrapt>=1.11.1 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.14.1)
Requirement already satisfied: protobuf>=3.6.1 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (3.19.6)
Requirement already satisfied: keras-applications>=1.0.6 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.0.8)
Requirement already satisfied: termcolor>=1.1.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.1.0)
Requirement already satisfied: grpcio>=1.8.6 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.48.2)
Requirement already satisfied: gast>=0.2.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (0.5.3)
Requirement already satisfied: tensorboard<1.15.0,>=1.14.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.14.0)
Requirement already satisfied: tensorflow-estimator<1.15.0rc0,>=1.14.0rc0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorflow==1.14->dso==1.0.dev0) (1.14.0)
Requirement already satisfied: importlib-metadata in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from click->dso==1.0.dev0) (4.8.3)
Requirement already satisfied: lark-parser<0.8.0,>=0.7.1 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from commentjson->dso==1.0.dev0) (0.7.8)
Requirement already satisfied: python-dateutil>=2.7.3 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pandas->dso==1.0.dev0) (2.8.2)
Requirement already satisfied: pytz>=2017.2 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pandas->dso==1.0.dev0) (2022.7)
Requirement already satisfied: ppft>=1.6.6.4 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pathos->dso==1.0.dev0) (1.6.6.4)
Requirement already satisfied: pox>=0.3.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pathos->dso==1.0.dev0) (0.3.0)
Requirement already satisfied: multiprocess>=0.70.12 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pathos->dso==1.0.dev0) (0.70.12.2)
Requirement already satisfied: dill>=0.3.4 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pathos->dso==1.0.dev0) (0.3.4)
Requirement already satisfied: iniconfig in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pytest->dso==1.0.dev0) (1.1.1)
Requirement already satisfied: pluggy<2.0,>=0.12 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pytest->dso==1.0.dev0) (1.0.0)
Requirement already satisfied: packaging in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pytest->dso==1.0.dev0) (21.3)
Requirement already satisfied: py>=1.8.2 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pytest->dso==1.0.dev0) (1.11.0)
Requirement already satisfied: attrs>=19.2.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pytest->dso==1.0.dev0) (22.2.0)
Requirement already satisfied: tomli>=1.0.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from pytest->dso==1.0.dev0) (1.2.3)
Requirement already satisfied: joblib>=0.11 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from scikit-learn->dso==1.0.dev0) (1.1.1)
Requirement already satisfied: scipy>=0.19.1 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from scikit-learn->dso==1.0.dev0) (1.5.4)
Requirement already satisfied: threadpoolctl>=2.0.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from scikit-learn->dso==1.0.dev0) (3.1.0)
Requirement already satisfied: matplotlib>=2.2 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from seaborn->dso==1.0.dev0) (3.3.4)
Requirement already satisfied: mpmath>=0.19 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from sympy->dso==1.0.dev0) (1.2.1)
Requirement already satisfied: importlib-resources in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tqdm->dso==1.0.dev0) (5.4.0)
Requirement already satisfied: typing-extensions>=3.6.4 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from importlib-metadata->click->dso==1.0.dev0) (4.1.1)
Requirement already satisfied: zipp>=0.5 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from importlib-metadata->click->dso==1.0.dev0) (3.6.0)
Requirement already satisfied: h5py in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from keras-applications>=1.0.6->tensorflow==1.14->dso==1.0.dev0) (3.1.0)
Requirement already satisfied: pillow>=6.2.0 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from matplotlib>=2.2->seaborn->dso==1.0.dev0) (8.4.0)
Requirement already satisfied: cycler>=0.10 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from matplotlib>=2.2->seaborn->dso==1.0.dev0) (0.11.0)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.3 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from matplotlib>=2.2->seaborn->dso==1.0.dev0) (3.0.9)
Requirement already satisfied: kiwisolver>=1.0.1 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from matplotlib>=2.2->seaborn->dso==1.0.dev0) (1.3.1)
Requirement already satisfied: markdown>=2.6.8 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorboard<1.15.0,>=1.14.0->tensorflow==1.14->dso==1.0.dev0) (3.3.7)
Requirement already satisfied: werkzeug>=0.11.15 in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from tensorboard<1.15.0,>=1.14.0->tensorflow==1.14->dso==1.0.dev0) (2.0.3)
Requirement already satisfied: dataclasses in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from werkzeug>=0.11.15->tensorboard<1.15.0,>=1.14.0->tensorflow==1.14->dso==1.0.dev0) (0.8)
Requirement already satisfied: cached-property in /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages (from h5py->keras-applications>=1.0.6->tensorflow==1.14->dso==1.0.dev0) (1.5.2)
Installing collected packages: dso
Running setup.py develop for dso
ERROR: Command errored out with exit status 1:
command: /Users/igor/Documents/ProjSymbReg/code/DSO_v2/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/igor/Downloads/deep-symbolic-optimization-master/dso/setup.py'"'"'; file='"'"'/Users/igor/Downloads/deep-symbolic-optimization-master/dso/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' develop --no-deps
cwd: /Users/igor/Downloads/deep-symbolic-optimization-master/dso/
Complete output (28 lines):
running develop
running egg_info
writing dso.egg-info/PKG-INFO
writing dependency_links to dso.egg-info/dependency_links.txt
writing requirements to dso.egg-info/requires.txt
writing top-level names to dso.egg-info/top_level.txt
reading manifest file 'dso.egg-info/SOURCES.txt'
writing manifest file 'dso.egg-info/SOURCES.txt'
running build_ext
building 'dso.cyfunc' extension
clang -DNDEBUG -g -fwrapv -O3 -Wall -I -I -I /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include -I /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include -I /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include -I -I/Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include -I/Users/igor/Documents/ProjSymbReg/code/DSO_v2/include -I/Users/igor/.pyenv/versions/3.6.15/include/python3.6m -I/Users/igor/Documents/ProjSymbReg/code/DSO_v2/include -I/Users/igor/.pyenv/versions/3.6.15/include/python3.6m -c dso/cyfunc.c -o build/temp.macosx-12.6-x86_64-3.6/dso/cyfunc.o
In file included from dso/cyfunc.c:759:
In file included from /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822:
/Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/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 "
^
1 warning generated.
clang -bundle -undefined dynamic_lookup -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/[email protected]/lib -L/Users/igor/.pyenv/versions/3.6.15/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/readline/lib -L/usr/local/opt/[email protected]/lib -L/Users/igor/.pyenv/versions/3.6.15/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -I -I -I /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include -I /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include -I /Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/numpy/core/include -I build/temp.macosx-12.6-x86_64-3.6/dso/cyfunc.o -o build/lib.macosx-12.6-x86_64-3.6/dso/cyfunc.cpython-36m-darwin.so
clang: error: no input files
/Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/setuptools/dist.py:493: UserWarning: Normalizing '1.0dev' to '1.0.dev0'
warnings.warn(tmpl.format(**locals()))
/Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/setuptools/command/easy_install.py:159: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
EasyInstallDeprecationWarning,
/Users/igor/Documents/ProjSymbReg/code/DSO_v2/lib/python3.6/site-packages/setuptools/command/install.py:37: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
setuptools.SetuptoolsDeprecationWarning,
error: command 'clang' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /Users/igor/Documents/ProjSymbReg/code/DSO_v2/bin/python3 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/igor/Downloads/deep-symbolic-optimization-master/dso/setup.py'"'"'; file='"'"'/Users/igor/Downloads/deep-symbolic-optimization-master/dso/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.
Any help would be appreciated.
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