auto-sklearn: Error during installation of pyrfr

I got the following error when installing pyrfr. What is installation directory here? My current directory?


(ml_env) ubuntu@ip-10-0-0-10:~/random_forest_run/build$ curl https://raw.githubusercontent.com/automl/auto-sklearn/master/requirements.txt | xargs -n 1 -L 1 pip install
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
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Requirement already satisfied: unittest2 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: six>=1.4 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from unittest2)
Requirement already satisfied: argparse in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from unittest2)
Requirement already satisfied: traceback2 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from unittest2)
Requirement already satisfied: linecache2 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from traceback2->unittest2)
Requirement already satisfied: setuptools in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages/setuptools-27.2.0-py3.6.egg
Requirement already satisfied: nose in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: six in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: Cython in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: numpy<1.12,>=1.9.0 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: scipy>=0.14.1 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: numpy>=1.8.2 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from scipy>=0.14.1)
Requirement already satisfied: scikit-learn==0.17.1 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: lockfile in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: joblib in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: psutil in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: pyyaml in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: ConfigArgParse in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: liac-arff in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: pandas in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: python-dateutil>=2 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from pandas)
Requirement already satisfied: pytz>=2011k in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from pandas)
Requirement already satisfied: numpy>=1.7.0 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from pandas)
Requirement already satisfied: six>=1.5 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from python-dateutil>=2->pandas)
Requirement already satisfied: xgboost==0.4a30 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: scipy in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from xgboost==0.4a30)
Requirement already satisfied: numpy in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from xgboost==0.4a30)
Requirement already satisfied: ConfigSpace<0.4,>=0.3.1 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: typing in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from ConfigSpace<0.4,>=0.3.1)
Requirement already satisfied: numpy in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from ConfigSpace<0.4,>=0.3.1)
Requirement already satisfied: argparse in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from ConfigSpace<0.4,>=0.3.1)
Requirement already satisfied: pyparsing in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from ConfigSpace<0.4,>=0.3.1)
Requirement already satisfied: pynisher>=0.4 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: docutils>=0.3 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from pynisher>=0.4)
Requirement already satisfied: psutil in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from pynisher>=0.4)
Requirement already satisfied: setuptools in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages/setuptools-27.2.0-py3.6.egg (from pynisher>=0.4)

Collecting pyrfr
  Using cached pyrfr-0.4.0.tar.gz
Building wheels for collected packages: pyrfr
  Running setup.py bdist_wheel for pyrfr ... error
  Complete output from command /home/ubuntu/anaconda3/envs/ml_env/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-axcsozeu/pyrfr/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 /tmp/tmpmdz8gclmpip-wheel- --python-tag cp36:
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.6
  creating build/lib.linux-x86_64-3.6/pyrfr
  copying pyrfr/__init__.py -> build/lib.linux-x86_64-3.6/pyrfr
  running build_ext
  building '_regression' extension
  swigging pyrfr/regression.i to pyrfr/regression_wrap.cpp
  swig -python -c++ -I${CMAKE_SOURCE_DIR}/include -I./include -o pyrfr/regression_wrap.cpp pyrfr/regression.i
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/pyrfr
  gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I${CMAKE_SOURCE_DIR}/include -I./include -I/home/ubuntu/anaconda3/envs/ml_env/include/python3.6m -c pyrfr/regression_wrap.cpp -o build/temp.linux-x86_64-3.6/pyrfr/regression_wrap.o -O2 -std=c++11
  cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
  g++ -pthread -shared -L/home/ubuntu/anaconda3/envs/ml_env/lib -Wl,-rpath=/home/ubuntu/anaconda3/envs/ml_env/lib,--no-as-needed build/temp.linux-x86_64-3.6/pyrfr/regression_wrap.o -L/home/ubuntu/anaconda3/envs/ml_env/lib -lpython3.6m -o build/lib.linux-x86_64-3.6/_regression.cpython-36m-x86_64-linux-gnu.so
  building '_util' extension
  swigging pyrfr/util.i to pyrfr/util_wrap.cpp
  swig -python -c++ -I${CMAKE_SOURCE_DIR}/include -I./include -o pyrfr/util_wrap.cpp pyrfr/util.i
  gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I${CMAKE_SOURCE_DIR}/include -I./include -I/home/ubuntu/anaconda3/envs/ml_env/include/python3.6m -c pyrfr/util_wrap.cpp -o build/temp.linux-x86_64-3.6/pyrfr/util_wrap.o -O2 -std=c++11
  cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]
  g++ -pthread -shared -L/home/ubuntu/anaconda3/envs/ml_env/lib -Wl,-rpath=/home/ubuntu/anaconda3/envs/ml_env/lib,--no-as-needed build/temp.linux-x86_64-3.6/pyrfr/util_wrap.o -L/home/ubuntu/anaconda3/envs/ml_env/lib -lpython3.6m -o build/lib.linux-x86_64-3.6/_util.cpython-36m-x86_64-linux-gnu.so
  installing to build/bdist.linux-x86_64/wheel
  running install
  running install_lib
  creating build/bdist.linux-x86_64
  creating build/bdist.linux-x86_64/wheel
  copying build/lib.linux-x86_64-3.6/_regression.cpython-36m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel
  creating build/bdist.linux-x86_64/wheel/pyrfr
  copying build/lib.linux-x86_64-3.6/pyrfr/__init__.py -> build/bdist.linux-x86_64/wheel/pyrfr
  copying build/lib.linux-x86_64-3.6/_util.cpython-36m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel
  running install_egg_info
  running egg_info
  writing pyrfr.egg-info/PKG-INFO
  writing dependency_links to pyrfr.egg-info/dependency_links.txt
  writing top-level names to pyrfr.egg-info/top_level.txt
  warning: manifest_maker: standard file '-c' not found
  
  reading manifest file 'pyrfr.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no files found matching '*.pxd' under directory 'pyrfr'
  warning: no files found matching '*.pyx' under directory 'pyrfr'
  warning: manifest_maker: MANIFEST.in, line 11: unknown action 'CMakeList.txt'
  
  writing manifest file 'pyrfr.egg-info/SOURCES.txt'
  Copying pyrfr.egg-info to build/bdist.linux-x86_64/wheel/pyrfr-0.4.0-py3.6.egg-info
  running install_scripts
  Checking .pth file support in build/bdist.linux-x86_64/wheel/
  /home/ubuntu/anaconda3/envs/ml_env/bin/python -E -c pass
  TEST FAILED: build/bdist.linux-x86_64/wheel/ does NOT support .pth files
  error: bad install directory or PYTHONPATH
  creating build/bdist.linux-x86_64/wheel/pyrfr
  copying build/lib.linux-x86_64-3.6/pyrfr/__init__.py -> build/bdist.linux-x86_64/wheel/pyrfr
  copying build/lib.linux-x86_64-3.6/_util.cpython-36m-x86_64-linux-gnu.so -> build/bdist.linux-x86_64/wheel
  running install_egg_info
  running egg_info
  writing pyrfr.egg-info/PKG-INFO
  writing dependency_links to pyrfr.egg-info/dependency_links.txt
  writing top-level names to pyrfr.egg-info/top_level.txt
  warning: manifest_maker: standard file '-c' not found 

  reading manifest file 'pyrfr.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'


      You are attempting to install a package to a directory that is not
      on PYTHONPATH and which Python does not read ".pth" files from.  The
      installation directory you specified (via --install-dir, --prefix, or
      the distutils default setting) was:
  
      build/bdist.linux-x86_64/wheel/


  and your PYTHONPATH environment variable currently contains:
  
      ''
  
  Here are some of your options for correcting the problem:
  
  * You can choose a different installation directory, i.e., one that is
    on PYTHONPATH or supports .pth files
  
  * You can add the installation directory to the PYTHONPATH environment
    variable.  (It must then also be on PYTHONPATH whenever you run
    Python and want to use the package(s) you are installing.)
  
  * You can set up the installation directory to support ".pth" files by
    using one of the approaches described here:
  
    https://setuptools.readthedocs.io/en/latest/easy_install.html#custom-installation-locations
  
  
  Please make the appropriate changes for your system and try again.
  
  ----------------------------------------
  Failed building wheel for pyrfr
  Running setup.py clean for pyrfr

Failed to build pyrfr
Installing collected packages: pyrfr
  Running setup.py install for pyrfr ... done
  Could not find .egg-info directory in install record for pyrfr from https://pypi.python.org/packages/21/4c/58533c51ab301f61d3521dc4cd29ba8145eed8f11b84f70aba9fd28f6aca/pyrfr-0.4.0.tar.gz#md5=70ccd2527bd85c18b8a65c7498d5e0de
Successfully installed pyrfr-0.4.0
Requirement already satisfied: smac==0.3.0 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages
Requirement already satisfied: numpy>=1.7.1 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: scipy>=0.18.1 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: scikit-learn in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: pyrfr in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: ConfigSpace>=0.3.1 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: pynisher>=0.4.1 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: psutil in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: typing in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: setuptools in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages/setuptools-27.2.0-py3.6.egg (from smac==0.3.0)
Requirement already satisfied: Cython in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: six in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from smac==0.3.0)
Requirement already satisfied: pyparsing in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from ConfigSpace>=0.3.1->smac==0.3.0)
Requirement already satisfied: argparse in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from ConfigSpace>=0.3.1->smac==0.3.0)
Requirement already satisfied: docutils>=0.3 in /home/ubuntu/anaconda3/envs/ml_env/lib/python3.6/site-packages (from pynisher>=0.4.1->smac==0.3.0)



About this issue

  • Original URL
  • State: closed
  • Created 7 years ago
  • Comments: 21 (9 by maintainers)

Most upvoted comments

Hello, I’m having the same problem pyrfr installation failure trying to install auto-sklearn@v.0.2.0. I’ve read through this thread several times but am still confused about how you recommend installing. It does not appear that a new version of pyrfr has been tagged since the last post.

The requirements.txt file on the auto-sklearn development branch still lists pyrfr>=0.4.0 as a dependency, but I can’t build pyrfr at all for the reasons listed above. I can, however, build pyrfr==0.2.0. So do you recommend installing development branch of auto-sklearn, but bypassing requirements.txt file and installing pyrfr 0.2.0? Or since pyrfr requirements do not seem to have changed between auto-sklearn v.0.2.0, to install auto-sklearn v.0.2.0 from PyPI but manually install pyrfr 0.2.0? Or something else? Thanks.