I need a Docker image that has both LibreOffice installed AND python pandas. I've decided that there's a bunch of licensing issues with LibreOffice now because the Oracle's JRE/JDK requirements. So, I'm starting FROM linuxserver/libreoffice:7.2.2 in my Docker image. Now, the problem is that when I try to install pandas using a virtual environment and a requirements.txt file (only line in it is pandas>=1.4.0,<1.5) like this:
ENV VIRTUAL_ENV=/opt/venv
RUN python3 -m venv $VIRTUAL_ENV
ENV PATH="$VIRTUAL_ENV/bin:$PATH"
# Install dependencies:
COPY requirements.txt .
RUN /opt/venv/bin/python3 -m pip install --upgrade pip && \
pip install -r requirements.txt
...I get this massive error:
#9 50.08 Collecting oldest-supported-numpy>=0.10
#9 50.08 Downloading oldest_supported_numpy-2022.4.18-py3-none-any.whl (3.9 kB)
#9 50.08 Collecting numpy==1.19.3
#9 50.08 Downloading numpy-1.19.3.zip (7.3 MB)
#9 50.08 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 2.3 MB/s eta 0:00:00
#9 50.08 Installing build dependencies: started
#9 50.08 Installing build dependencies: finished with status 'done'
#9 50.08 Getting requirements to build wheel: started
#9 50.08 Getting requirements to build wheel: finished with status 'done'
#9 50.08 Preparing metadata (pyproject.toml): started
#9 50.08 Preparing metadata (pyproject.toml): finished with status 'error'
#9 50.08 error: subprocess-exited-with-error
#9 50.08
#9 50.08 × Preparing metadata (pyproject.toml) did not run successfully.
#9 50.08 │ exit code: 1
#9 50.08 ╰─> [236 lines of output]
#9 50.08 Running from numpy source directory.
#9 50.08 setup.py:480: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
#9 50.08 run_build = parse_setuppy_commands()
#9 50.08 Processing numpy/random/_bounded_integers.pxd.in
#9 50.08 Processing numpy/random/_pcg64.pyx
#9 50.08 Processing numpy/random/_philox.pyx
#9 50.08 Processing numpy/random/mtrand.pyx
#9 50.08 Processing numpy/random/_generator.pyx
#9 50.08 Processing numpy/random/_common.pyx
#9 50.08 Processing numpy/random/_mt19937.pyx
#9 50.08 Processing numpy/random/_sfc64.pyx
#9 50.08 Processing numpy/random/_bounded_integers.pyx.in
#9 50.08 Processing numpy/random/bit_generator.pyx
#9 50.08 Cythonizing sources
#9 50.08 blas_opt_info:
#9 50.08 blas_mkl_info:
#9 50.08 customize UnixCCompiler
#9 50.08 libraries mkl_rt not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 blis_info:
#9 50.08 libraries blis not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 openblas_info:
#9 50.08 libraries openblas not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 atlas_3_10_blas_threads_info:
#9 50.08 Setting PTATLAS=ATLAS
#9 50.08 libraries tatlas not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 atlas_3_10_blas_info:
#9 50.08 libraries satlas not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 atlas_blas_threads_info:
#9 50.08 Setting PTATLAS=ATLAS
#9 50.08 libraries ptf77blas,ptcblas,atlas not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 atlas_blas_info:
#9 50.08 libraries f77blas,cblas,atlas not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 accelerate_info:
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 /tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/system_info.py:1914: UserWarning:
#9 50.08 Optimized (vendor) Blas libraries are not found.
#9 50.08 Falls back to netlib Blas library which has worse performance.
#9 50.08 A better performance should be easily gained by switching
#9 50.08 Blas library.
#9 50.08 if self._calc_info(blas):
#9 50.08 blas_info:
#9 50.08 libraries blas not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 /tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/system_info.py:1914: UserWarning:
#9 50.08 Blas (http://www.netlib.org/blas/) libraries not found.
#9 50.08 Directories to search for the libraries can be specified in the
#9 50.08 numpy/distutils/site.cfg file (section [blas]) or by setting
#9 50.08 the BLAS environment variable.
#9 50.08 if self._calc_info(blas):
#9 50.08 blas_src_info:
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 /tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/system_info.py:1914: UserWarning:
#9 50.08 Blas (http://www.netlib.org/blas/) sources not found.
#9 50.08 Directories to search for the sources can be specified in the
#9 50.08 numpy/distutils/site.cfg file (section [blas_src]) or by setting
#9 50.08 the BLAS_SRC environment variable.
#9 50.08 if self._calc_info(blas):
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 non-existing path in 'numpy/distutils': 'site.cfg'
#9 50.08 lapack_opt_info:
#9 50.08 lapack_mkl_info:
#9 50.08 libraries mkl_rt not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 openblas_lapack_info:
#9 50.08 libraries openblas not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 openblas_clapack_info:
#9 50.08 libraries openblas,lapack not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 flame_info:
#9 50.08 libraries flame not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 atlas_3_10_threads_info:
#9 50.08 Setting PTATLAS=ATLAS
#9 50.08 libraries lapack_atlas not found in /opt/venv/lib
#9 50.08 libraries tatlas,tatlas not found in /opt/venv/lib
#9 50.08 libraries lapack_atlas not found in /usr/local/lib
#9 50.08 libraries tatlas,tatlas not found in /usr/local/lib
#9 50.08 libraries lapack_atlas not found in /usr/lib
#9 50.08 libraries tatlas,tatlas not found in /usr/lib
#9 50.08 <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 atlas_3_10_info:
#9 50.08 libraries lapack_atlas not found in /opt/venv/lib
#9 50.08 libraries satlas,satlas not found in /opt/venv/lib
#9 50.08 libraries lapack_atlas not found in /usr/local/lib
#9 50.08 libraries satlas,satlas not found in /usr/local/lib
#9 50.08 libraries lapack_atlas not found in /usr/lib
#9 50.08 libraries satlas,satlas not found in /usr/lib
#9 50.08 <class 'numpy.distutils.system_info.atlas_3_10_info'>
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 atlas_threads_info:
#9 50.08 Setting PTATLAS=ATLAS
#9 50.08 libraries lapack_atlas not found in /opt/venv/lib
#9 50.08 libraries ptf77blas,ptcblas,atlas not found in /opt/venv/lib
#9 50.08 libraries lapack_atlas not found in /usr/local/lib
#9 50.08 libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
#9 50.08 libraries lapack_atlas not found in /usr/lib
#9 50.08 libraries ptf77blas,ptcblas,atlas not found in /usr/lib
#9 50.08 <class 'numpy.distutils.system_info.atlas_threads_info'>
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 atlas_info:
#9 50.08 libraries lapack_atlas not found in /opt/venv/lib
#9 50.08 libraries f77blas,cblas,atlas not found in /opt/venv/lib
#9 50.08 libraries lapack_atlas not found in /usr/local/lib
#9 50.08 libraries f77blas,cblas,atlas not found in /usr/local/lib
#9 50.08 libraries lapack_atlas not found in /usr/lib
#9 50.08 libraries f77blas,cblas,atlas not found in /usr/lib
#9 50.08 <class 'numpy.distutils.system_info.atlas_info'>
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 lapack_info:
#9 50.08 libraries lapack not found in ['/opt/venv/lib', '/usr/local/lib', '/usr/lib']
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 /tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/system_info.py:1748: UserWarning:
#9 50.08 Lapack (http://www.netlib.org/lapack/) libraries not found.
#9 50.08 Directories to search for the libraries can be specified in the
#9 50.08 numpy/distutils/site.cfg file (section [lapack]) or by setting
#9 50.08 the LAPACK environment variable.
#9 50.08 return getattr(self, '_calc_info_{}'.format(name))()
#9 50.08 lapack_src_info:
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 /tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/system_info.py:1748: UserWarning:
#9 50.08 Lapack (http://www.netlib.org/lapack/) sources not found.
#9 50.08 Directories to search for the sources can be specified in the
#9 50.08 numpy/distutils/site.cfg file (section [lapack_src]) or by setting
#9 50.08 the LAPACK_SRC environment variable.
#9 50.08 return getattr(self, '_calc_info_{}'.format(name))()
#9 50.08 NOT AVAILABLE
#9 50.08
#9 50.08 numpy_linalg_lapack_lite:
#9 50.08 FOUND:
#9 50.08 language = c
#9 50.08 define_macros = [('HAVE_BLAS_ILP64', None), ('BLAS_SYMBOL_SUFFIX', '64_')]
#9 50.08
#9 50.08 /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
#9 50.08 warnings.warn(msg)
#9 50.08 running dist_info
#9 50.08 running build_src
#9 50.08 build_src
#9 50.08 building py_modules sources
#9 50.08 creating build
#9 50.08 creating build/src.linux-x86_64-3.9
#9 50.08 creating build/src.linux-x86_64-3.9/numpy
#9 50.08 creating build/src.linux-x86_64-3.9/numpy/distutils
#9 50.08 building library "npymath" sources
#9 50.08 Could not locate executable gfortran
#9 50.08 Could not locate executable f95
#9 50.08 Could not locate executable ifort
#9 50.08 Could not locate executable ifc
#9 50.08 Could not locate executable lf95
#9 50.08 Could not locate executable pgfortran
#9 50.08 Could not locate executable nvfortran
#9 50.08 Could not locate executable f90
#9 50.08 Could not locate executable f77
#9 50.08 Could not locate executable fort
#9 50.08 Could not locate executable efort
#9 50.08 Could not locate executable efc
#9 50.08 Could not locate executable g77
#9 50.08 Could not locate executable g95
#9 50.08 Could not locate executable pathf95
#9 50.08 Could not locate executable nagfor
#9 50.08 don't know how to compile Fortran code on platform 'posix'
#9 50.08 Traceback (most recent call last):
#9 50.08 File "/tmp/tmpqq2gyha2_in_process.py", line 363, in <module>
#9 50.08 main()
#9 50.08 File "/tmp/tmpqq2gyha2_in_process.py", line 345, in main
#9 50.08 json_out['return_val'] = hook(**hook_input['kwargs'])
#9 50.08 File "/tmp/tmpqq2gyha2_in_process.py", line 164, in prepare_metadata_for_build_wheel
#9 50.08 return hook(metadata_directory, config_settings)
#9 50.08 File "/tmp/pip-build-env-6370icr8/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 157, in prepare_metadata_for_build_wheel
#9 50.08 self.run_setup()
#9 50.08 File "/tmp/pip-build-env-6370icr8/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 248, in run_setup
#9 50.08 super(_BuildMetaLegacyBackend,
#9 50.08 File "/tmp/pip-build-env-6370icr8/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 142, in run_setup
#9 50.08 exec(compile(code, __file__, 'exec'), locals())
#9 50.08 File "setup.py", line 508, in <module>
#9 50.08 setup_package()
#9 50.08 File "setup.py", line 500, in setup_package
#9 50.08 setup(**metadata)
#9 50.08 File "/tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/core.py", line 169, in setup
#9 50.08 return old_setup(**new_attr)
#9 50.08 File "/tmp/pip-build-env-6370icr8/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 165, in setup
#9 50.08 return distutils.core.setup(**attrs)
#9 50.08 File "/usr/lib/python3.9/distutils/core.py", line 148, in setup
#9 50.08 dist.run_commands()
#9 50.08 File "/usr/lib/python3.9/distutils/dist.py", line 966, in run_commands
#9 50.08 self.run_command(cmd)
#9 50.08 File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
#9 50.08 cmd_obj.run()
#9 50.08 File "/tmp/pip-build-env-6370icr8/overlay/lib/python3.9/site-packages/setuptools/command/dist_info.py", line 31, in run
#9 50.08 egg_info.run()
#9 50.08 File "/tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/command/egg_info.py", line 24, in run
#9 50.08 self.run_command("build_src")
#9 50.08 File "/usr/lib/python3.9/distutils/cmd.py", line 313, in run_command
#9 50.08 self.distribution.run_command(command)
#9 50.08 File "/usr/lib/python3.9/distutils/dist.py", line 985, in run_command
#9 50.08 cmd_obj.run()
#9 50.08 File "/tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/command/build_src.py", line 144, in run
#9 50.08 self.build_sources()
#9 50.08 File "/tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/command/build_src.py", line 155, in build_sources
#9 50.08 self.build_library_sources(*libname_info)
#9 50.08 File "/tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/command/build_src.py", line 288, in build_library_sources
#9 50.08 sources = self.generate_sources(sources, (lib_name, build_info))
#9 50.08 File "/tmp/pip-install-m9ffqtsd/numpy_f52b823899c842e29073892fb891d2ea/numpy/distutils/command/build_src.py", line 378, in generate_sources
#9 50.08 source = func(extension, build_dir)
#9 50.08 File "numpy/core/setup.py", line 663, in get_mathlib_info
#9 50.08 raise RuntimeError("Broken toolchain: cannot link a simple C program")
#9 50.08 RuntimeError: Broken toolchain: cannot link a simple C program
#9 50.08 [end of output]
#9 50.08
#9 50.08 note: This error originates from a subprocess, and is likely not a problem with pip.
#9 50.08 error: metadata-generation-failed
#9 50.08
#9 50.08 × Encountered error while generating package metadata.
#9 50.08 ╰─> See above for output.
#9 50.08
#9 50.08 note: This is an issue with the package mentioned above, not pip.
#9 50.08 hint: See above for details.
#9 50.08 [end of output]
#9 50.08
#9 50.08 note: This error originates from a subprocess, and is likely not a problem with pip.
#9 50.09 error: subprocess-exited-with-error
#9 50.09
#9 50.09 × pip subprocess to install build dependencies did not run successfully.
#9 50.09 │ exit code: 1
#9 50.09 ╰─> See above for output.
#9 50.09
#9 50.09 note: This error originates from a subprocess, and is likely not a problem with pip.
------
executor failed running [/bin/sh -c /opt/venv/bin/python3 -m pip install --upgrade pip && pip install -r requirements.txt]: exit code: 1
I've looked around at several answers listed here that seem very similar to what I'm getting, but this discussion seems pretty old and out of date. None of the solutions I've tried from there are working.
It looks like BLAS and a couple of other items aren't installed correctly on the Alpine image. I've tried a bunch of different ways to do this and none have worked so far. How can I install pandas on this Alpine Docker image?
UPDATE
I'd be willing to use a Debian or Ubuntu-based Docker image as long as it comes preloaded with LibreOffice. The only image I've found online, so far, that comes with LibreOffice preloaded is an Alpine image...
I think you can use openjdk, but I'm not sure.
As for pandas, it's missing BLAS C libraries that can only be installed with apk. You can do that easily by running apk add openblas, but you might need also the openblas-dev package as well.
Related
I thought specifying -DCMAKE_CXX_COMPILER_FORCED=1 -DCMAKE_C_COMPILER_FORCED=1 for cmake would make my build faster, because it would skip compiler checks. Instead, it makes my build fail:
#16 470.8 -- Found Git: /usr/bin/git (found version "2.17.1")
#16 470.8 -- Content of the error:
#16 470.8 -- Version of this git repo: v0.0.1-2-g93b2a22
#16 470.9 -- The C compiler identification is GNU 5.5.0
#16 470.9 -- The CXX compiler identification is GNU 5.5.0
#16 470.9 -- GCC detected - Adding flags
#16 471.0 -- Looking for pthread.h
#16 471.0 -- Looking for pthread.h - found
#16 471.0 -- Looking for pthread_create
#16 471.1 -- Looking for pthread_create - not found
#16 471.1 -- Looking for pthread_create in pthreads
#16 471.1 -- Looking for pthread_create in pthreads - not found
#16 471.1 -- Looking for pthread_create in pthread
#16 471.2 -- Looking for pthread_create in pthread - found
#16 471.2 -- Found Threads: TRUE
#16 471.2 -- Found Protobuf: /usr/local/lib/libprotobuf.so;-lpthread (found version "3.5.0")
#16 471.2 CMake Error at /opt/cmake/share/cmake-3.12/Modules/FindBoost.cmake:2048 (message):
#16 471.2 Unable to find the requested Boost libraries.
#16 471.2
#16 471.2 Boost version: 1.65.1
#16 471.2
#16 471.2 Boost include path: /usr/include
#16 471.2
#16 471.2 Could not find the following Boost libraries:
#16 471.2
#16 471.2 boost_graph
#16 471.2
#16 471.2 No Boost libraries were found. You may need to set BOOST_LIBRARYDIR to the
#16 471.2 directory containing Boost libraries or BOOST_ROOT to the location of
#16 471.2 Boost.
#16 471.2 Call Stack (most recent call first):
#16 471.2 CMakeLists.txt:24 (find_package)
#16 471.2
#16 471.2
#16 471.3 -- Configuring incomplete, errors occurred!
libboost-graph-dev is installed, so it's unclear what is happening here - if I remove the options, then the build is working.
What is happening here?
From the docs:
The Boost Graph Library is a header-only library and does not need to
be built to be used.
Header only libraries need not to be specified in the find_package(Boost ...) call. Remove it and instead link either to the target Boost::boost in your target_link_libraries call
or add include_directories(${Boost_INCLUDE_DIRS}) to your CMakeLists.txt file.
I was trying to run spyder with tensorflow-gpu and managed to setup tensorflow-gpu through conda in anaconda prompt. However post this step when i try to install keras, i get the following error:
(tenserflow-gpu) C:\Users\Nithin\Documents>pip install keras
Collecting keras
Downloading Keras-2.0.8-py2.py3-none-any.whl (276kB)
100% |################################| 276kB 161kB/s
Collecting scipy>=0.14 (from keras)
Downloading scipy-0.19.1.tar.gz (14.1MB)
100% |################################| 14.1MB 465kB/s
Requirement already satisfied: numpy>=1.9.1 in c:\users\nithin\appdata\local\conda\conda\envs\tenserflow-gpu\lib\site-packages (from keras)
Requirement already satisfied: six>=1.9.0 in c:\users\nithin\appdata\local\conda\conda\envs\tenserflow-gpu\lib\site-packages (from keras)
Collecting pyyaml (from keras)
Downloading PyYAML-3.12-cp35-cp35m-win_amd64.whl (195kB)
100% |################################| 204kB 308kB/s
Building wheels for collected packages: scipy
Running setup.py bdist_wheel for scipy ... error
Complete output from command C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\Nithin\\AppData\\Local\\Temp\\pip-build-ju_zavf1\\scipy\\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 C:\Users\Nithin\AppData\Local\Temp\tmpuhtgm8rppip-wheel- --python-tag cp35:
lapack_opt_info:
lapack_mkl_info:
libraries mkl_rt not found in ['C:\\Users\\Nithin\\AppData\\Local\\conda\\conda\\envs\\tenserflow-gpu\\lib', 'C:\\', 'C:\\Users\\Nithin\\AppData\\Local\\conda\\conda\\envs\\tenserflow-gpu\\libs']
NOT AVAILABLE
openblas_lapack_info:
C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\system_info.py:655: UserWarning: Specified path c:\opt\64\lib is invalid.
return self.get_paths(self.section, key)
libraries libopenblas_v0.2.20_mingwpy not found in []
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries tatlas,tatlas not found in C:\
libraries lapack_atlas not found in C:\
libraries tatlas,tatlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries satlas,satlas not found in C:\
libraries lapack_atlas not found in C:\
libraries satlas,satlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries ptf77blas,ptcblas,atlas not found in C:\
libraries lapack_atlas not found in C:\
libraries ptf77blas,ptcblas,atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries f77blas,cblas,atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries f77blas,cblas,atlas not found in C:\
libraries lapack_atlas not found in C:\
libraries f77blas,cblas,atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
lapack_info:
libraries lapack not found in ['C:\\Users\\Nithin\\AppData\\Local\\conda\\conda\\envs\\tenserflow-gpu\\lib', 'C:\\', 'C:\\Users\\Nithin\\AppData\\Local\\conda\\conda\\envs\\tenserflow-gpu\\libs']
NOT AVAILABLE
C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
self.calc_info()
lapack_src_info:
NOT AVAILABLE
C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
self.calc_info()
NOT AVAILABLE
Running from scipy source directory.
non-existing path in 'scipy\\integrate': 'quadpack.h'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\Nithin\AppData\Local\Temp\pip-build-ju_zavf1\scipy\setup.py", line 416, in <module>
setup_package()
File "C:\Users\Nithin\AppData\Local\Temp\pip-build-ju_zavf1\scipy\setup.py", line 412, in setup_package
setup(**metadata)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\core.py", line 135, in setup
config = configuration()
File "C:\Users\Nithin\AppData\Local\Temp\pip-build-ju_zavf1\scipy\setup.py", line 336, in configuration
config.add_subpackage('scipy')
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 1029, in add_subpackage
caller_level = 2)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 998, in get_subpackage
caller_level = caller_level + 1)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 935, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 1029, in add_subpackage
caller_level = 2)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 998, in get_subpackage
caller_level = caller_level + 1)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 935, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\linalg\setup.py", line 20, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
----------------------------------------
Failed building wheel for scipy
Running setup.py clean for scipy
Complete output from command C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\Nithin\\AppData\\Local\\Temp\\pip-build-ju_zavf1\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all:
`setup.py clean` is not supported, use one of the following instead:
- `git clean -xdf` (cleans all files)
- `git clean -Xdf` (cleans all versioned files, doesn't touch
files that aren't checked into the git repo)
Add `--force` to your command to use it anyway if you must (unsupported).
----------------------------------------
Failed cleaning build dir for scipy
Failed to build scipy
Installing collected packages: scipy, pyyaml, keras
Running setup.py install for scipy ... error
Complete output from command C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\Nithin\\AppData\\Local\\Temp\\pip-build-ju_zavf1\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\Nithin\AppData\Local\Temp\pip-9xcwjndr-record\install-record.txt --single-version-externally-managed --compile:
Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:
- `pip install .` (from a git repo or downloaded source
release)
- `pip install scipy` (last SciPy release on PyPI)
lapack_opt_info:
lapack_mkl_info:
libraries mkl_rt not found in ['C:\\Users\\Nithin\\AppData\\Local\\conda\\conda\\envs\\tenserflow-gpu\\lib', 'C:\\', 'C:\\Users\\Nithin\\AppData\\Local\\conda\\conda\\envs\\tenserflow-gpu\\libs']
NOT AVAILABLE
openblas_lapack_info:
C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\system_info.py:655: UserWarning: Specified path c:\opt\64\lib is invalid.
return self.get_paths(self.section, key)
libraries libopenblas_v0.2.20_mingwpy not found in []
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries tatlas,tatlas not found in C:\
libraries lapack_atlas not found in C:\
libraries tatlas,tatlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries satlas,satlas not found in C:\
libraries lapack_atlas not found in C:\
libraries satlas,satlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries ptf77blas,ptcblas,atlas not found in C:\
libraries lapack_atlas not found in C:\
libraries ptf77blas,ptcblas,atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries f77blas,cblas,atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib
libraries f77blas,cblas,atlas not found in C:\
libraries lapack_atlas not found in C:\
libraries f77blas,cblas,atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
libraries lapack_atlas not found in C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\libs
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
lapack_info:
libraries lapack not found in ['C:\\Users\\Nithin\\AppData\\Local\\conda\\conda\\envs\\tenserflow-gpu\\lib', 'C:\\', 'C:\\Users\\Nithin\\AppData\\Local\\conda\\conda\\envs\\tenserflow-gpu\\libs']
NOT AVAILABLE
C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
self.calc_info()
lapack_src_info:
NOT AVAILABLE
C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
self.calc_info()
NOT AVAILABLE
Running from scipy source directory.
non-existing path in 'scipy\\integrate': 'quadpack.h'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\Nithin\AppData\Local\Temp\pip-build-ju_zavf1\scipy\setup.py", line 416, in <module>
setup_package()
File "C:\Users\Nithin\AppData\Local\Temp\pip-build-ju_zavf1\scipy\setup.py", line 412, in setup_package
setup(**metadata)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\core.py", line 135, in setup
config = configuration()
File "C:\Users\Nithin\AppData\Local\Temp\pip-build-ju_zavf1\scipy\setup.py", line 336, in configuration
config.add_subpackage('scipy')
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 1029, in add_subpackage
caller_level = 2)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 998, in get_subpackage
caller_level = caller_level + 1)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 935, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 1029, in add_subpackage
caller_level = 2)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 998, in get_subpackage
caller_level = caller_level + 1)
File "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\lib\site-packages\numpy\distutils\misc_util.py", line 935, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\linalg\setup.py", line 20, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
----------------------------------------
Command "C:\Users\Nithin\AppData\Local\conda\conda\envs\tenserflow-gpu\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\Nithin\\AppData\\Local\\Temp\\pip-build-ju_zavf1\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\Nithin\AppData\Local\Temp\pip-9xcwjndr-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\Nithin\AppData\Local\Temp\pip-build-ju_zavf1\scipy\
(tenserflow-gpu) C:\Users\Nithin\Documents>
In conda i downgraded python to 3.5.2 from 3.6.2 as tensorflow-gpu would only work with 3.5.2.
Could some one please help. Thanks in advance.
Python 3.5 on Windows 7
Modules installed: Numpy (1.11.1), Pandas (0.18.1), Matplotlib (1.5.1)
Pip version: 8.1.2
I'm installing many of the standard packages, and was able to install the 3 packages above without problems. Scipy's installation is not working however. After some searching on the issue through the 2 links below, I upgraded pip to the newest version. This hasn't fixed the issue, and I'm a bit lost.
From what I can gather, I'm missing lapack and numpy distutils files. I'm not familiar with lapack, and I installed the latest numpy just today. Perhaps I need to reset some paths and directories?
2 links I used for trouble shooting:
Python pip install fails: invalid command egg_info
Can't install Scipy through pip
Apologies for posting such a huge block of code, but I thought it would be best to include everything the error gives me.
Collecting scipy
Using cached scipy-0.17.1.tar.gz
Installing collected packages: scipy
Running setup.py install for scipy ... error
Complete output from command c:\users\jon\appdata\local\programs\python\pyth
on35-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\Jon\\
AppData\\Local\\Temp\\pip-build-ugbb8uwx\\scipy\\setup.py';exec(compile(getattr(
tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'
))" install --record C:\Users\Jon\AppData\Local\Temp\pip-uh3v7wvi-record\install
-record.txt --single-version-externally-managed --compile:
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['c:\\users\\jon\\appdata\\local\\programs
\\python\\python35-32\\lib', 'C:\\', 'c:\\users\\jon\\appdata\\local\\programs\\
python\\python35-32\\libs']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['c:\\users\\jon\\appdata\\local\\pro
grams\\python\\python35-32\\lib', 'C:\\', 'c:\\users\\jon\\appdata\\local\\progr
ams\\python\\python35-32\\libs']
NOT AVAILABLE
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
c:\users\jon\appdata\local\programs\python\python35-32\lib\site-packages\num
py\distutils\system_info.py:639: UserWarning: Specified path C:\projects\windows
-wheel-builder\atlas-builds\atlas-3.10.1-sse2-32\lib is invalid.
warnings.warn('Specified path %s is invalid.' % d)
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
c:\users\jon\appdata\local\programs\python\python35-32\lib\site-packages\num
py\distutils\system_info.py:1548: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
libraries lapack not found in ['c:\\users\\jon\\appdata\\local\\programs\\
python\\python35-32\\lib', 'C:\\', 'c:\\users\\jon\\appdata\\local\\programs\\py
thon\\python35-32\\libs']
NOT AVAILABLE
c:\users\jon\appdata\local\programs\python\python35-32\lib\site-packages\num
py\distutils\system_info.py:1559: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
NOT AVAILABLE
c:\users\jon\appdata\local\programs\python\python35-32\lib\site-packages\num
py\distutils\system_info.py:1562: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
NOT AVAILABLE
Running from scipy source directory.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "C:\Users\Jon\AppData\Local\Temp\pip-build-ugbb8uwx\scipy\setup.py",
line 265, in <module>
setup_package()
File "C:\Users\Jon\AppData\Local\Temp\pip-build-ugbb8uwx\scipy\setup.py",
line 262, in setup_package
setup(**metadata)
File "c:\users\jon\appdata\local\programs\python\python35-32\lib\site-pack
ages\numpy\distutils\core.py", line 135, in setup
config = configuration()
File "C:\Users\Jon\AppData\Local\Temp\pip-build-ugbb8uwx\scipy\setup.py",
line 182, in configuration
config.add_subpackage('scipy')
File "c:\users\jon\appdata\local\programs\python\python35-32\lib\site-pack
ages\numpy\distutils\misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "c:\users\jon\appdata\local\programs\python\python35-32\lib\site-pack
ages\numpy\distutils\misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "c:\users\jon\appdata\local\programs\python\python35-32\lib\site-pack
ages\numpy\distutils\misc_util.py", line 909, in _get_configuration_from_setup_p
y
config = setup_module.configuration(*args)
File "scipy\setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "c:\users\jon\appdata\local\programs\python\python35-32\lib\site-pack
ages\numpy\distutils\misc_util.py", line 1003, in add_subpackage
caller_level = 2)
File "c:\users\jon\appdata\local\programs\python\python35-32\lib\site-pack
ages\numpy\distutils\misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "c:\users\jon\appdata\local\programs\python\python35-32\lib\site-pack
ages\numpy\distutils\misc_util.py", line 909, in _get_configuration_from_setup_p
y
config = setup_module.configuration(*args)
File "scipy\linalg\setup.py", line 20, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
----------------------------------------
Command "c:\users\jon\appdata\local\programs\python\python35-32\python.exe -u -c
"import setuptools, tokenize;__file__='C:\\Users\\Jon\\AppData\\Local\\Temp\\pi
p-build-ugbb8uwx\\scipy\\setup.py';exec(compile(getattr(tokenize, 'open', open)(
__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\
Users\Jon\AppData\Local\Temp\pip-uh3v7wvi-record\install-record.txt --single-ver
sion-externally-managed --compile" failed with error code 1 in C:\Users\Jon\AppD
ata\Local\Temp\pip-build-ugbb8uwx\scipy\
Trying to install numpy for pypy3 on my MacBook, I receive an error.
Here are the instructions to install numpy.
git clone https://bitbucket.org/pypy/numpy.git
cd numpy
pypy3 setup.py install
But when I launch "pypy3 setup.py install, I receive this error message:
Running from numpy source directory.
/usr/local/Cellar/pypy3/2.4.0/libexec/lib_pypy/__pycache__/_cffi__g93a4bf4dxace1544d.c:2:10: fatal error:
'stdio.h' file not found
#include <stdio.h>
^
1 error generated.
/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/dist.py:257: UserWarning: Unknown distribution option: 'test_suite'
warnings.warn(msg)
non-existing path in 'numpy/distutils': 'site.cfg'
non-existing path in 'numpy/f2py': 'docs'
non-existing path in 'numpy/f2py': 'f2py.1'
F2PY Version 2
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in ['/usr/local/Cellar/pypy3/2.4.0/libexec/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
openblas_info:
libraries openblas not found in ['/usr/local/Cellar/pypy3/2.4.0/libexec/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/Cellar/pypy3/2.4.0/libexec/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/usr/local/Cellar/pypy3/2.4.0/libexec/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
FOUND:
extra_compile_args = ['-msse3', '-I/System/Library/Frameworks/vecLib.framework/Headers']
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
non-existing path in 'numpy/lib': 'benchmarks'
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['/usr/local/Cellar/pypy3/2.4.0/libexec/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['/usr/local/Cellar/pypy3/2.4.0/libexec/lib', '/usr/local/lib', '/usr/lib']
NOT AVAILABLE
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in /usr/local/Cellar/pypy3/2.4.0/libexec/lib
libraries lapack_atlas not found in /usr/local/Cellar/pypy3/2.4.0/libexec/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries f77blas,cblas,atlas not found in /usr/local/Cellar/pypy3/2.4.0/libexec/lib
libraries lapack_atlas not found in /usr/local/Cellar/pypy3/2.4.0/libexec/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
FOUND:
extra_compile_args = ['-msse3']
extra_link_args = ['-Wl,-framework', '-Wl,Accelerate']
define_macros = [('NO_ATLAS_INFO', 3)]
/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/dist.py:257: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
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 py_modules sources
building library "npymath" sources
customize Gnu95FCompiler
Found executable /usr/local/bin/gfortran
/Users/remioudin/numpy/numpy/distutils/fcompiler/gnu.py:129: UserWarning: Env. variable MACOSX_DEPLOYMENT_TARGET set to 10.3
warnings.warn(s)
customize Gnu95FCompiler
customize Gnu95FCompiler using config
C compiler: cc -arch x86_64 -O2 -fPIC -Wimplicit -O2 -fPIC -Wimplicit
compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -I/usr/local/Cellar/pypy3/2.4.0/libexec/include -c'
cc: _configtest.c
cc -arch x86_64 _configtest.o -o _configtest
ld: library not found for -lcrt1.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
ld: library not found for -lcrt1.o
clang: error: linker command failed with exit code 1 (use -v to see invocation)
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "setup.py", line 251, in <module>
setup_package()
File "setup.py", line 243, in setup_package
setup(**metadata)
File "/Users/remioudin/numpy/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/dist.py", line 917, in run_commands
self.run_command(cmd)
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/dist.py", line 936, in run_command
cmd_obj.run()
File "/Users/remioudin/numpy/numpy/distutils/command/install.py", line 60, in run
r = old_install.run(self)
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/command/install.py", line 579, in run
self.run_command('build')
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/dist.py", line 936, in run_command
cmd_obj.run()
File "/Users/remioudin/numpy/numpy/distutils/command/build.py", line 39, in run
old_build.run(self)
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/command/build.py", line 126, in run
self.run_command(cmd_name)
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/Cellar/pypy3/2.4.0/libexec/lib-python/3/distutils/dist.py", line 936, in run_command
cmd_obj.run()
File "/Users/remioudin/numpy/numpy/distutils/command/build_src.py", line 153, in run
self.build_sources()
File "/Users/remioudin/numpy/numpy/distutils/command/build_src.py", line 164, in build_sources
self.build_library_sources(*libname_info)
File "/Users/remioudin/numpy/numpy/distutils/command/build_src.py", line 299, in build_library_sources
sources = self.generate_sources(sources, (lib_name, build_info))
File "/Users/remioudin/numpy/numpy/distutils/command/build_src.py", line 386, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 688, in get_mathlib_info
raise RuntimeError("Broken toolchain: cannot link a simple C program")
RuntimeError: Broken toolchain: cannot link a simple C program
Do you have an idea of what is the problem?
You're right...
Numpy is available only for Pypy 2.5.0, which is compatible with Python 2.7.
I actually use Python 3.4.2, so all my files are compatible with pypy3 and not pypy.
I will do without numpy then...
Hope they will manage to make it work for pypy3 in the next few months!
https://bitbucket.org/pypy/numpy - Have you verified with pypy that their version of numpy works with pypy3? A quick read of their site suggests it is still in the works.
For now, NumPyPy only works with Python 2, and is not complete. You may get warnings or NotImplemented errors. Please let us know if you get crashes or wrong results.
I have successfully installed anaconda on Windows 7.
Pandas and numpy work fine with IPython notebook and I have verified that anaconda is referenced on the PATH.
Yet, I can not install the pandas package wothin Pycharm.
I am not sure how to proceed.
Install packages failed: Error occurred when installing package pandas.
The following command was executed:
packaging_tool.py install --build-dir C:\Users\mferrini\AppData\Local\Temp\pycharm-packaging5585301427553978431.tmp pandas
The error output of the command:
Downloading/unpacking pandas
Running setup.py egg_info for package pandas
non-existing path in 'numpy\\distutils': 'site.cfg'
non-existing path in 'numpy\\f2py': 'docs'
non-existing path in 'numpy\\f2py': 'f2py.1'
non-existing path in 'numpy\\lib': 'benchmarks'
Running from numpy source directory.
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1526: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1535: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
warnings.warn(BlasNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1538: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
warnings.warn(BlasSrcNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1432: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1443: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1446: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
C:\Python27\lib\distutils\dist.py:267: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
Traceback (most recent call last):
File "<string>", line 16, in <module>
File "C:\Users\mferrini\AppData\Local\Temp\pycharm-packaging5585301427553978431.tmp\pandas\setup.py", line 619, in <module>
**setuptools_kwargs)
File "C:\Python27\lib\distutils\core.py", line 111, in setup
_setup_distribution = dist = klass(attrs)
File "build\bdist.win32\egg\setuptools\dist.py", line 239, in __init__
File "build\bdist.win32\egg\setuptools\dist.py", line 263, in fetch_build_eggs
File "build\bdist.win32\egg\pkg_resources.py", line 568, in resolve
File "build\bdist.win32\egg\pkg_resources.py", line 806, in best_match
File "build\bdist.win32\egg\pkg_resources.py", line 818, in obtain
File "build\bdist.win32\egg\setuptools\dist.py", line 313, in fetch_build_egg
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 609, in easy_install
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 639, in install_item
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 825, in install_eggs
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 1031, in build_and_install
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 1019, in run_setup
distutils.errors.DistutilsError: Setup script exited with error: Unable to find vcvarsall.bat
Complete output from command python setup.py egg_info:
non-existing path in 'numpy\\distutils': 'site.cfg'
non-existing path in 'numpy\\f2py': 'docs'
non-existing path in 'numpy\\f2py': 'f2py.1'
non-existing path in 'numpy\\lib': 'benchmarks'
Running from numpy source directory.
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1526: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1535: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
warnings.warn(BlasNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1538: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
warnings.warn(BlasSrcNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1432: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1443: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
c:\users\mferrini\appdata\local\temp\easy_install-gartid\numpy-1.9.1\numpy\distutils\system_info.py:1446: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
C:\Python27\lib\distutils\dist.py:267: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
Traceback (most recent call last):
File "<string>", line 16, in <module>
File "C:\Users\mferrini\AppData\Local\Temp\pycharm-packaging5585301427553978431.tmp\pandas\setup.py", line 619, in <module>
**setuptools_kwargs)
File "C:\Python27\lib\distutils\core.py", line 111, in setup
_setup_distribution = dist = klass(attrs)
File "build\bdist.win32\egg\setuptools\dist.py", line 239, in __init__
File "build\bdist.win32\egg\setuptools\dist.py", line 263, in fetch_build_eggs
File "build\bdist.win32\egg\pkg_resources.py", line 568, in resolve
File "build\bdist.win32\egg\pkg_resources.py", line 806, in best_match
File "build\bdist.win32\egg\pkg_resources.py", line 818, in obtain
File "build\bdist.win32\egg\setuptools\dist.py", line 313, in fetch_build_egg
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 609, in easy_install
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 639, in install_item
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 825, in install_eggs
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 1031, in build_and_install
File "build\bdist.win32\egg\setuptools\command\easy_install.py", line 1019, in run_setup
distutils.errors.DistutilsError: Setup script exited with error: Unable to find vcvarsall.bat
----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in C:\Users\mferrini\AppData\Local\Temp\pycharm-packaging5585301427553978431.tmp\pandas
Storing complete log in C:\Users\mferrini\pip\pip.log