Installation failure with conflicting error messages.
mar-ses opened this issue · 3 comments
mar-ses commented
Following the installation instructions I tried first using the pip method (on two computers). First one worked (Ubuntu 16.10), second one failed (Ubuntu 14.04, but similar python environment) with the following error code (copy pasting the relevant part):
gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -I/home/marko/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/include/eigen3 -I./hodlr/header -I/home/marko/anaconda3/include/python3.5m -c george/_kernels.cpp -o build/temp.linux-x86_64-3.5/george/_kernels.o -Wno-unused-function -Wno-uninitialized
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Failed building wheel for george
Running setup.py clean for george
Failed to build george
Installing collected packages: george
Running setup.py install for george ... error
Complete output from command /home/marko/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-qf6ggi46/george/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-is44ebst-record/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/george
copying george/utils.py -> build/lib.linux-x86_64-3.5/george
copying george/kernels.py -> build/lib.linux-x86_64-3.5/george
copying george/gp.py -> build/lib.linux-x86_64-3.5/george
copying george/generate_kernel_defs.py -> build/lib.linux-x86_64-3.5/george
copying george/__init__.py -> build/lib.linux-x86_64-3.5/george
copying george/basic.py -> build/lib.linux-x86_64-3.5/george
creating build/lib.linux-x86_64-3.5/george/testing
copying george/testing/test_solvers.py -> build/lib.linux-x86_64-3.5/george/testing
copying george/testing/test_tutorial.py -> build/lib.linux-x86_64-3.5/george/testing
copying george/testing/test_gp.py -> build/lib.linux-x86_64-3.5/george/testing
copying george/testing/__init__.py -> build/lib.linux-x86_64-3.5/george/testing
copying george/testing/test_pickle.py -> build/lib.linux-x86_64-3.5/george/testing
copying george/testing/test_kernels.py -> build/lib.linux-x86_64-3.5/george/testing
running egg_info
writing dependency_links to george.egg-info/dependency_links.txt
writing top-level names to george.egg-info/top_level.txt
writing george.egg-info/PKG-INFO
warning: manifest_maker: standard file '-c' not found
reading manifest file 'george.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'george.egg-info/SOURCES.txt'
copying george/_kernels.cpp -> build/lib.linux-x86_64-3.5/george
copying george/hodlr.cpp -> build/lib.linux-x86_64-3.5/george
running build_ext
Found Eigen version 3.2.0 in: /usr/include/eigen3
Found HODLR headers in: ./hodlr/header
building 'george._kernels' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/george
gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Iinclude -I/home/marko/anaconda3/lib/python3.5/site-packages/numpy/core/include -I/usr/include/eigen3 -I./hodlr/header -I/home/marko/anaconda3/include/python3.5m -c george/_kernels.cpp -o build/temp.linux-x86_64-3.5/george/_kernels.o -Wno-unused-function -Wno-uninitialized
gcc: error trying to exec 'cc1plus': execvp: No such file or directory
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/home/marko/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-qf6ggi46/george/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-is44ebst-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-qf6ggi46/george/
I think it's relevant that it seems to find "HODLR" on my machine Found HODLR headers in: ./hodlr/header
So I tried installing the development version by cloning off github, and then I get the following error:
running build_ext
Found Eigen version 3.2.0 in: /usr/include/eigen3
Traceback (most recent call last):
File "setup.py", line 177, in <module>
"Programming Language :: Python",
File "/home/marko/anaconda3/lib/python3.5/distutils/core.py", line 148, in setup
dist.run_commands()
File "/home/marko/anaconda3/lib/python3.5/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/home/marko/anaconda3/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/marko/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/setuptools/command/install.py", line 67, in run
File "/home/marko/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/setuptools/command/install.py", line 109, in do_egg_install
File "/home/marko/anaconda3/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/marko/anaconda3/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/marko/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/setuptools/command/bdist_egg.py", line 161, in run
File "/home/marko/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/setuptools/command/bdist_egg.py", line 147, in call_command
File "/home/marko/anaconda3/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/marko/anaconda3/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/marko/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/setuptools/command/install_lib.py", line 11, in run
File "/home/marko/anaconda3/lib/python3.5/distutils/command/install_lib.py", line 107, in build
self.run_command('build_ext')
File "/home/marko/anaconda3/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/marko/anaconda3/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/home/marko/anaconda3/lib/python3.5/site-packages/setuptools-27.2.0-py3.5.egg/setuptools/command/build_ext.py", line 77, in run
File "/home/marko/anaconda3/lib/python3.5/site-packages/Cython/Distutils/build_ext.py", line 164, in run
_build_ext.build_ext.run(self)
File "/home/marko/anaconda3/lib/python3.5/distutils/command/build_ext.py", line 338, in run
self.build_extensions()
File "/home/marko/anaconda3/lib/python3.5/site-packages/Cython/Distutils/build_ext.py", line 172, in build_extensions
self.build_extension(ext)
File "setup.py", line 99, in build_extension
raise RuntimeError("Required library HODLR not found. "
RuntimeError: Required library HODLR not found. Check the documentation for solutions.
Which seems contradictory as it found HODLR the first time. Also I didn't understand the first error message.
dfm commented
I'm not sure what's up with the first one but the second error is because you didn't run:
git submodule init
git submodule update
This is not a contradiction because HODLR is a submodule in the development version.
mar-ses commented
Sorry I must have skimmed through that my bad. However, now trying the development version seems to be giving me the same error message as in the first case, gcc failing to exec 'cc1plus': execvp. Is this some dependency that I need to download?
mar-ses commented
My bad, hadn't install g++ apparently. Doing that made it work.