PICRUSt Installation on Ubuntu 14.04 LTS

[Ali Faruqi]

Hi everyone!

So, I've managed to successfully install PICRUSt on Ubuntu 14.04 LTS. However, when I try out a couple of different scripts, I get ImportError of Python particularly in importing functions from biom, even though I have biom installed on the machine. Following are few examples of the errors I am facing:

afaruqi@dombak:~$ normalize_by_copy_number.py -h
Traceback (most recent call last):
  File "/usr/local/bin/normalize_by_copy_number.py", line 16, in <module>
    from biom.parse import parse_biom_table, parse_classic_table_to_rich_table
ImportError: cannot import name parse_classic_table_to_rich_table
afaruqi@dombak:~$ predict_metagenomes.py -h
Traceback (most recent call last):
  File "/usr/local/bin/predict_metagenomes.py", line 17, in <module>
    from picrust.predict_metagenomes import predict_metagenomes,predict_metagenome_variances,\
  File "/usr/local/lib/python2.7/dist-packages/picrust/predict_metagenomes.py", line 15, in <module>
    from biom.table import table_factory,SparseGeneTable, DenseGeneTable
ImportError: cannot import name table_factory
afaruqi@dombak:~$ metagenome_contributions.py -h
Traceback (most recent call last):
  File "/usr/local/bin/metagenome_contributions.py", line 18, in <module>
    from picrust.predict_metagenomes import predict_metagenomes, calc_nsti
  File "/usr/local/lib/python2.7/dist-packages/picrust/predict_metagenomes.py", line 15, in <module>
    from biom.table import table_factory,SparseGeneTable, DenseGeneTable
ImportError: cannot import name table_factory
afaruqi@dombak:~$ biom
usage: biom <command> [<args>]
The currently available commands are:
   add-metadata        Add metadata to a BIOM table
   convert             Convert to/from the BIOM table format
   normalize-table     Normalize a BIOM table
   show-install-info   Provide information about the biom-format installation
   subset-table        Subset a BIOM table
   summarize-table     Summarize sample or observation data in a BIOM table
   validate-table      Validate a BIOM-formatted file
See 'biom help <command>' for more information on a specific command.

I'd greatly appreciate if the problem can be resolved. Thank you very much.

Best,

Ali 

[Ali Faruqi]

Hello,

My colleague pointed out to an older discussion on the forum:

https://groups.google.com/forum/#!topic/picrust-users/ZGQewXcllOw

I have BIOM version 2.1.3, which I removed and reinstalled BIOM 1.3.1. PICRUSt works now but QIIME seems to be broken. Anyway, just want to know when will PICRUSt become updated to be used with the newest version of BIOM? Please let me know. Thanks a lot.

Ali

[Ali Faruqi]

Thanks to the developers of QIIME, who pointed that I should use virtualenvwrapper to have separate installations QIIME and PICRUSt, I was able to successfully install PICRUSt and QIIME together using different virtualenvs. Following are the steps for PICRUSt, which may be of use to the community users. Thanks.

# virtualenv for PICRUSt

sudo pip install virtualenvwrapper
sudo mkdir /usr/local/Envs/
sudo chmod -R 777 /usr/local/Envs/
export WORKON_HOME=/usr/local/Envs/
mkdir -p $WORKON_HOME
sudo cp /usr/local/bin/virtualenvwrapper.sh /etc/profile.d/
source /etc/profile.d/virtualenvwrapper.sh
mkvirtualenv env1
pip install numpy==1.5.1
pip install pyqi 

# BIOM for PICRUSt
wget https://pypi.python.org/packages/source/b/biom-format/biom-format-1.3.1.tar.gz
tar -xvzf biom-format-1.3.1.tar.gz
sudo mv biom-format-1.3.1.tar.gz biom-format-1.3.1
cd biom-format-1.3.1/ 
sudo python setup.py build
sudo python setup.py install 

# PyCogent for PICRUSt
wget http://pycogent.org/_downloads/cogent-requirements.txt
DONT_USE_PYREX=1 pip install -r cogent-requirements.txt 

PICRUSt (1.0.0):

wget https://github.com/picrust/picrust/releases/download/1.0.0/picrust-1.0.0.tar.gz
tar -xzf picrust-1.0.0.tar.gz
mv picrust-1.0.0.tar.gz picrust-1.0.0
wget ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/16S_13_5_precalculated.tab.gz
wget ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/ko_13_5_precalculated.tab.gz
mkdir picrust-1.0.0/picrust/data
sudo mv ko_13_5_precalculated.tab.gz picrust-1.0.0/picrust/data
sudo mv 16S_13_5_precalculated.tab.gz picrust-1.0.0/picrust/data
cd picrust-1.0.0/
python setup.py install    

[Jesse Zaneveld]

Glad the virtualenv solution worked for you and thanks for sharing!

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[Kassi Kosnicki]

Hi Ali,

Thank you for posting this as I have really had the run-around in using both QIIME and PICRUSt on the same computer due to their incompatible dependencies. Your directions are pretty straight forward, however when you are first installing the virtualenv, are you installing the virtualenvwrapper while you're in /usr/local/bin/ directory?  I'm getting an error  when I copy (
sudo cp /usr/local/bin/virtualenvwrapper.sh /etc/profile.d/) the wrapper.

Thanks,
Kassi

[Ali Ahmad Faruqi]

Hi Kassi,

Thanks for your email. Yeah, from my instructions it seems that the virtualenvwrapper.sh shell script was present in /usr/local/bin directory. Can you tell me what error you are getting? Also, unfortunately, I don't have access to a Linux machine currently, so I can't validate these steps.

On a side note, I'd now think that I'd now prefer managing virtual environments through conda rather than virtualenvwrapper.sh. You can find conda installation instructions here.

Thanks and let me know if conda helps.

Best,

Ali

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[Kassi Kosnicki]

Hi Ali,
This is a great help. However, I am running this on OS X, using a unix terminal. Also, I've installed a python2 environment, however I have done so using Anaconda version 1.4. With this not be compatible since it requires Anaconda3? I'm noticing that I can't use the get and module commands which I'm assuming is due to not having the proper anaconda installed or is this a linux command?

Thanks for your help,
Kassi

[Ali Ahmad Faruqi]

Hi Kassi,

Can you please post the exact commands you are using and the error messages you are getting? This will help me troubleshoot better and give better advice.

Thanks a bunch,

Ali

[Kassi Kosnicki]

So, I've installed everything I need and am currently working in the python2 environment. However, when I load qiime 1.8 I get this error:

(python2) MacBook-Air:picrust kassikosnicki$ module load qiime/1.8.0
-bash: module: command not found


Should I not be in picrust?
Also, I have not downloaded qiime 1.8 as I currently have 1.9 on my computer and am actively using it. I was hoping that using this environment would not jeopardize the installation of the 1.9 version. Any advice would be greatly appreciated.

So I proceeded to exit picrust and try to install "module" and got this error.
(python2) MacBook-Air:~ kassikosnicki$ conda install module
Fetching package metadata ....Error: HTTPError: 500 Server Error: Internal Server Error for url: https://repo.continuum.io/pkgs/free/noarch/repodata.json.bz2: https://repo.continuum.io/pkgs/free/noarch/

UGHHH. Dependencies are killing me. It's too bad picrust can't just use the latest versions of biom, etc.

Thanks again for your help,
Kassi

Should I

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[Ali Ahmad Faruqi]

Hi Kassi,

Thanks for your detailed message. I'm not aware of what the 'module' package does that you are trying to install via conda. In lieu of that, I have tried to install PICRUSt on my Mac using conda. Following are specifications of the my conda, Python and Mac and the individual steps with which I used to successfully install PICRUSt on Mac:

conda 4.1.6 with Python 2.7.12 for Mac OS X El Capitan Version 10.11.4. 

I assume you have sudo permissions, load up a new terminal window and do the following steps:

# Create a new environment call picrust_env

# Install numpy and wget pacakges

conda create -n picrust_env numpy==1.5.1 wget

source activate picrust_env

# Install pyqi, cogent and biom separately, since it's causing problem

pip install pyqi cogent==1.5.3 biom-format==1.3.1 

PICRUSt (1.0.0):

# curl not retreiving the whole file for some reason

python -c 'import wget; wget.download("https://github.com/picrust/picrust/releases/download/1.0.0/picrust-1.0.0.tar.gz")'

tar -xzvf picrust-1.0.0.tar.gz

mv picrust-1.0.0.tar.gz picrust-1.0.0

python -c 'import wget; wget.download("ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/16S_13_5_precalculated.tab.gz")'

# This step will take some time

python -c 'import wget; wget.download("ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/ko_13_5_precalculated.tab.gz")'

mkdir picrust-1.0.0/picrust/data

mv ko_13_5_precalculated.tab.gz picrust-1.0.0/picrust/data

mv 16S_13_5_precalculated.tab.gz picrust-1.0.0/picrust/data

cd picrust-1.0.0/

python setup.py install

Hope this helps and works.

Lastly, PICRUSt and QIIME should have their own separate virtual environments. You cannot have both QIIME and PICRUSt in same virtual environment to work.

I know it's a bit of a pain switching between two environments but at the moment, this is the solution I see. Maybe PICRUSt developers can better comment on when they plan to update their BIOM version. Thanks a lot.

Cheers,

Ali

[clair...@gmail.com]

Hi Ali,

Thank you for sharing. I came across the same error like you. and I follow your instructions of installing PICRSt using virtualenv. but I didn't reinstall QIIME using virtualenv. at last, the same error came out.

I'm a new starter in Linux. and I can't figure out why. Is it because I didn't reinstall QIIME using virtualenv? If so, shall uninstall QIIME first?

Thanks,

Jia

在 2015年4月28日星期二 UTC+8上午5:34:48，Ali Faruqi写道：

[Ali Ahmad Faruqi]

Hi Jia,

It's hard to say what the issue is without knowing the exact message you are getting, your system specs, etc. The basic idea is that you should have QIIME and PICRUSt in separate environments, so that they can use different versions of BIOM. 

My personal preference, currently, would be to use conda to have a different virtual environment for PICRUSt and a different virtual environment for QIIME. Other people can chip in with their suggestions.

Thanks a bunch,

Ali

--

[clair...@gmail.com]

Hi Ali,

Thank you for your prompt reply. Now I'm installing the QIIME and PICRUSt under two different virtual environments. And QIIME has been installed successfully. But I still came across a problem with numpy installation when I tried to install PICRUSt following your instruction.

when I install "pip install numpy==1.5.1", the error came out as list below. I checked the packages installed in this virtual environment, and found numpy has already installed.It is "numpy-1.11.1". Do you have any idea how to solve this problem?

Thanks,

Jia

jiaxu@neerjalinux4:~$ pip install numpy==1.5.1

Collecting numpy==1.5.1

/usr/local/Envs/env1/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:318: SNIMissingWarning: An HTTPS request has been made, but the SNI (Subject Name Indication) extension to TLS is not available on this platform. This may cause the server to present an incorrect TLS certificate, which can cause validation failures. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#snimissingwarning.

  SNIMissingWarning

/usr/local/Envs/env1/local/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:122: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. You can upgrade to a newer version of Python to solve this. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.

  InsecurePlatformWarning

  Using cached numpy-1.5.1.tar.gz

Building wheels for collected packages: numpy

  Running setup.py bdist_wheel for numpy ... [?25l- \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | error

  Complete output from command /usr/local/Envs/env1/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-zMlE9D/numpy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d /tmp/tmp760Zhopip-wheel- --python-tag cp27:

  Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'

  F2PY Version 1

  blas_opt_info:

  blas_mkl_info:

    libraries mkl,vml,guide not found in /usr/local/Envs/env1/lib

    libraries mkl,vml,guide not found in /usr/local/lib

    libraries mkl,vml,guide not found in /usr/lib

    NOT AVAILABLE

  

  atlas_blas_threads_info:

  Setting PTATLAS=ATLAS

    libraries ptf77blas,ptcblas,atlas not found in /usr/local/Envs/env1/lib

    libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

    libraries ptf77blas,ptcblas,atlas not found in /usr/lib

    NOT AVAILABLE

  

  atlas_blas_info:

    libraries f77blas,cblas,atlas not found in /usr/local/Envs/env1/lib

    libraries f77blas,cblas,atlas not found in /usr/local/lib

    libraries f77blas,cblas,atlas not found in /usr/lib

    NOT AVAILABLE

  

  /tmp/pip-build-zMlE9D/numpy/numpy/distutils/system_info.py:1399: 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__)

  blas_info:

    FOUND:

      libraries = ['blas']

      library_dirs = ['/usr/local/Envs/env1/lib']

      language = f77

  

    FOUND:

      libraries = ['blas']

      library_dirs = ['/usr/local/Envs/env1/lib']

      define_macros = [('NO_ATLAS_INFO', 1)]

      language = f77

  

  lapack_opt_info:

  lapack_mkl_info:

  mkl_info:

    libraries mkl,vml,guide not found in /usr/local/Envs/env1/lib

    libraries mkl,vml,guide not found in /usr/local/lib

    libraries mkl,vml,guide not found in /usr/lib

    NOT AVAILABLE

  

    NOT AVAILABLE

  

  atlas_threads_info:

  Setting PTATLAS=ATLAS

    libraries ptf77blas,ptcblas,atlas not found in /usr/local/Envs/env1/lib

    libraries lapack_atlas not found in /usr/local/Envs/env1/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

  numpy.distutils.system_info.atlas_threads_info

    NOT AVAILABLE

  

  atlas_info:

    libraries f77blas,cblas,atlas not found in /usr/local/Envs/env1/lib

    libraries lapack_atlas not found in /usr/local/Envs/env1/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

  numpy.distutils.system_info.atlas_info

    NOT AVAILABLE

  

  /tmp/pip-build-zMlE9D/numpy/numpy/distutils/system_info.py:1306: 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:

    FOUND:

      libraries = ['lapack']

      library_dirs = ['/usr/local/Envs/env1/lib']

      language = f77

  

    FOUND:

      libraries = ['lapack', 'blas']

      library_dirs = ['/usr/local/Envs/env1/lib']

      define_macros = [('NO_ATLAS_INFO', 1)]

      language = f77

  

  running bdist_wheel

  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 GnuFCompiler

  Could not locate executable g77

  Could not locate executable f77

  customize IntelFCompiler

  Could not locate executable ifort

  Could not locate executable ifc

  customize LaheyFCompiler

  Could not locate executable lf95

  customize PGroupFCompiler

  Could not locate executable pgf90

  Could not locate executable pgf77

  customize AbsoftFCompiler

  Could not locate executable f90

  customize NAGFCompiler

  Found executable /usr/bin/f95

  customize VastFCompiler

  customize CompaqFCompiler

  Could not locate executable fort

  customize IntelItaniumFCompiler

  Could not locate executable efort

  Could not locate executable efc

  customize IntelEM64TFCompiler

  customize Gnu95FCompiler

  Found executable /usr/bin/gfortran

  customize Gnu95FCompiler

  customize Gnu95FCompiler using config

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  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/include -I/usr/include/python2.7 -c'

  x86_64-linux-gnu-gcc: _configtest.c

  x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest

  success!

  removing: _configtest.c _configtest.o _configtest

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  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/include -I/usr/include/python2.7 -c'

  x86_64-linux-gnu-gcc: _configtest.c

  _configtest.c:1:5: warning: conflicting types for built-in function 鈥榚xp鈥?[enabled by default]

   int exp (void);

       ^

  x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest

  _configtest.o: In function `main':

  /tmp/pip-build-zMlE9D/numpy/_configtest.c:6: undefined reference to `exp'

  collect2: error: ld returned 1 exit status

  _configtest.o: In function `main':

  /tmp/pip-build-zMlE9D/numpy/_configtest.c:6: undefined reference to `exp'

  collect2: error: ld returned 1 exit status

  failure.

  removing: _configtest.c _configtest.o

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  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/include -I/usr/include/python2.7 -c'

  x86_64-linux-gnu-gcc: _configtest.c

  _configtest.c:1:5: warning: conflicting types for built-in function 鈥榚xp鈥?[enabled by default]

   int exp (void);

       ^

  x86_64-linux-gnu-gcc -pthread _configtest.o -lm -o _configtest

  success!

  removing: _configtest.c _configtest.o _configtest

  building extension "numpy.core._sort" sources

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.

  executing numpy/core/code_generators/generate_numpy_api.py

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.

  numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h']

  building extension "numpy.core.multiarray" sources

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.

  executing numpy/core/code_generators/generate_numpy_api.py

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.

  numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h']

  building extension "numpy.core.umath" sources

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.

  executing numpy/core/code_generators/generate_ufunc_api.py

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources.

    adding 'build/src.linux-x86_64-2.7/numpy/core/src/umath' to include_dirs.

  numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/umath/funcs.inc', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h']

  building extension "numpy.core.scalarmath" sources

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.

  executing numpy/core/code_generators/generate_numpy_api.py

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.

  executing numpy/core/code_generators/generate_ufunc_api.py

    adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources.

  numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h']

  building extension "numpy.core._dotblas" sources

  building extension "numpy.core.umath_tests" sources

  building extension "numpy.core.multiarray_tests" sources

  building extension "numpy.lib._compiled_base" sources

  building extension "numpy.numarray._capi" sources

  building extension "numpy.fft.fftpack_lite" sources

  building extension "numpy.linalg.lapack_lite" sources

    adding 'numpy/linalg/lapack_litemodule.c' to sources.

    adding 'numpy/linalg/python_xerbla.c' to sources.

  building extension "numpy.random.mtrand" sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  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/include -I/usr/include/python2.7 -c'

  x86_64-linux-gnu-gcc: _configtest.c

  x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest

  _configtest

  failure.

  removing: _configtest.c _configtest.o _configtest

  building data_files sources

  build_src: building npy-pkg config files

  running build_py

  creating build/lib.linux-x86_64-2.7

  creating build/lib.linux-x86_64-2.7/numpy

  copying numpy/__init__.py -> build/lib.linux-x86_64-2.7/numpy

  copying numpy/_import_tools.py -> build/lib.linux-x86_64-2.7/numpy

  copying numpy/setupscons.py -> build/lib.linux-x86_64-2.7/numpy

  copying numpy/matlib.py -> build/lib.linux-x86_64-2.7/numpy

  copying numpy/version.py -> build/lib.linux-x86_64-2.7/numpy

  copying numpy/dual.py -> build/lib.linux-x86_64-2.7/numpy

  copying numpy/setup.py -> build/lib.linux-x86_64-2.7/numpy

  copying numpy/add_newdocs.py -> build/lib.linux-x86_64-2.7/numpy

  copying numpy/ctypeslib.py -> build/lib.linux-x86_64-2.7/numpy

  copying build/src.linux-x86_64-2.7/numpy/__config__.py -> build/lib.linux-x86_64-2.7/numpy

  creating build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/core.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/__init__.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/ccompiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/environment.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/system_info.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/log.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/exec_command.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/__version__.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/compat.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/mingw32ccompiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/intelccompiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/from_template.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/extension.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/interactive.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/lib2def.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/line_endings.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/conv_template.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/setup.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/cpuinfo.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/misc_util.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/unixccompiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/info.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/numpy_distribution.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying numpy/distutils/npy_pkg_config.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  copying build/src.linux-x86_64-2.7/numpy/distutils/__config__.py -> build/lib.linux-x86_64-2.7/numpy/distutils

  creating build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/__init__.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/install_data.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/egg_info.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/install.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/build.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/build_clib.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/build_ext.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/scons.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/build_scripts.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/config_compiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/install_headers.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/config.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/sdist.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/build_py.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/autodist.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/develop.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/install_clib.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/bdist_rpm.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  copying numpy/distutils/command/build_src.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

  creating build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/__init__.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/vast.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/g95.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/none.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/hpux.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/ibm.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/absoft.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/intel.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/sun.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/compaq.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/mips.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/lahey.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/pg.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/gnu.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  copying numpy/distutils/fcompiler/nag.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

  creating build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/__init__.py -> build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/nosetester.py -> build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/utils.py -> build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/noseclasses.py -> build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/nulltester.py -> build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/setup.py -> build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/decorators.py -> build/lib.linux-x86_64-2.7/numpy/testing

  copying numpy/testing/numpytest.py -> build/lib.linux-x86_64-2.7/numpy/testing

  creating build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/f90mod_rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/__init__.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/cfuncs.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/__version__.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/f2py_testing.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/func2subr.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/diagnose.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/cb_rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/common_rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/auxfuncs.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/capi_maps.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/setup.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/crackfortran.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/info.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/use_rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  copying numpy/f2py/f2py2e.py -> build/lib.linux-x86_64-2.7/numpy/f2py

  creating build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/numerictypes.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/machar.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/records.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/__init__.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/scons_support.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/numeric.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/setup_common.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/shape_base.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/fromnumeric.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/_mx_datetime_parser.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/_internal.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/function_base.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/setup.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/defchararray.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/memmap.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/getlimits.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/arrayprint.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/info.py -> build/lib.linux-x86_64-2.7/numpy/core

  copying numpy/core/code_generators/generate_numpy_api.py -> build/lib.linux-x86_64-2.7/numpy/core

  creating build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/financial.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/user_array.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/ufunclike.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/__init__.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/recfunctions.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/arrayterator.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/_datasource.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/scimath.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/utils.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/shape_base.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/stride_tricks.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/format.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/npyio.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/function_base.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/twodim_base.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/index_tricks.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/setup.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/type_check.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/arraysetops.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/_iotools.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/info.py -> build/lib.linux-x86_64-2.7/numpy/lib

  copying numpy/lib/polynomial.py -> build/lib.linux-x86_64-2.7/numpy/lib

  creating build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/ufuncs.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/user_array.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/__init__.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/linear_algebra.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/rng_stats.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/fix_default_axis.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/alter_code2.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/alter_code1.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/array_printer.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/matrix.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/compat.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/arrayfns.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/fft.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/functions.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/typeconv.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/setup.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/misc.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/precision.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/rng.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/ma.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/random_array.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  copying numpy/oldnumeric/mlab.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

  creating build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/numerictypes.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/ufuncs.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/__init__.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/linear_algebra.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/nd_image.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/alter_code2.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/alter_code1.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/session.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/matrix.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/util.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/compat.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/fft.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/functions.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/setup.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/convolve.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/ma.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/random_array.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/image.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  copying numpy/numarray/mlab.py -> build/lib.linux-x86_64-2.7/numpy/numarray

  creating build/lib.linux-x86_64-2.7/numpy/fft

  copying numpy/fft/__init__.py -> build/lib.linux-x86_64-2.7/numpy/fft

  copying numpy/fft/fftpack.py -> build/lib.linux-x86_64-2.7/numpy/fft

  copying numpy/fft/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/fft

  copying numpy/fft/helper.py -> build/lib.linux-x86_64-2.7/numpy/fft

  copying numpy/fft/setup.py -> build/lib.linux-x86_64-2.7/numpy/fft

  copying numpy/fft/info.py -> build/lib.linux-x86_64-2.7/numpy/fft

  creating build/lib.linux-x86_64-2.7/numpy/linalg

  copying numpy/linalg/__init__.py -> build/lib.linux-x86_64-2.7/numpy/linalg

  copying numpy/linalg/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/linalg

  copying numpy/linalg/linalg.py -> build/lib.linux-x86_64-2.7/numpy/linalg

  copying numpy/linalg/setup.py -> build/lib.linux-x86_64-2.7/numpy/linalg

  copying numpy/linalg/info.py -> build/lib.linux-x86_64-2.7/numpy/linalg

  creating build/lib.linux-x86_64-2.7/numpy/random

  copying numpy/random/__init__.py -> build/lib.linux-x86_64-2.7/numpy/random

  copying numpy/random/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/random

  copying numpy/random/setup.py -> build/lib.linux-x86_64-2.7/numpy/random

  copying numpy/random/info.py -> build/lib.linux-x86_64-2.7/numpy/random

  creating build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/core.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/mrecords.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/__init__.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/testutils.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/timer_comparison.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/bench.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/extras.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/version.py -> build/lib.linux-x86_64-2.7/numpy/ma

  copying numpy/ma/setup.py -> build/lib.linux-x86_64-2.7/numpy/ma

  creating build/lib.linux-x86_64-2.7/numpy/matrixlib

  copying numpy/matrixlib/__init__.py -> build/lib.linux-x86_64-2.7/numpy/matrixlib

  copying numpy/matrixlib/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/matrixlib

  copying numpy/matrixlib/setup.py -> build/lib.linux-x86_64-2.7/numpy/matrixlib

  copying numpy/matrixlib/defmatrix.py -> build/lib.linux-x86_64-2.7/numpy/matrixlib

  creating build/lib.linux-x86_64-2.7/numpy/compat

  copying numpy/compat/__init__.py -> build/lib.linux-x86_64-2.7/numpy/compat

  copying numpy/compat/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/compat

  copying numpy/compat/py3k.py -> build/lib.linux-x86_64-2.7/numpy/compat

  copying numpy/compat/_inspect.py -> build/lib.linux-x86_64-2.7/numpy/compat

  copying numpy/compat/setup.py -> build/lib.linux-x86_64-2.7/numpy/compat

  creating build/lib.linux-x86_64-2.7/numpy/polynomial

  copying numpy/polynomial/__init__.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

  copying numpy/polynomial/polytemplate.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

  copying numpy/polynomial/polyutils.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

  copying numpy/polynomial/chebyshev.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

  copying numpy/polynomial/setup.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

  copying numpy/polynomial/polynomial.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

  creating build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/basics.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/ufuncs.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/__init__.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/internals.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/subclassing.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/methods_vs_functions.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/byteswapping.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/structured_arrays.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/howtofind.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/creation.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/misc.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/jargon.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/performance.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/indexing.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/broadcasting.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/glossary.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/io.py -> build/lib.linux-x86_64-2.7/numpy/doc

  copying numpy/doc/constants.py -> build/lib.linux-x86_64-2.7/numpy/doc

  running build_clib

  customize UnixCCompiler

  customize UnixCCompiler using build_clib

  building 'npymath' library

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7

  creating build/temp.linux-x86_64-2.7/build

  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7

  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy

  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core

  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src

  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/npymath

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c

  x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math.c

  x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math_complex.c

  ar: adding 3 object files to build/temp.linux-x86_64-2.7/libnpymath.a

  running build_ext

  customize UnixCCompiler

  customize UnixCCompiler using build_ext

  customize GnuFCompiler

  customize IntelFCompiler

  customize LaheyFCompiler

  customize PGroupFCompiler

  customize AbsoftFCompiler

  customize NAGFCompiler

  customize VastFCompiler

  customize CompaqFCompiler

  customize IntelItaniumFCompiler

  customize IntelEM64TFCompiler

  customize Gnu95FCompiler

  customize Gnu95FCompiler

  customize Gnu95FCompiler using build_ext

  building 'numpy.core._sort' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.c

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.o -Lbuild/temp.linux-x86_64-2.7 -lm -o build/lib.linux-x86_64-2.7/numpy/core/_sort.so

  building 'numpy.core.multiarray' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7/numpy

  creating build/temp.linux-x86_64-2.7/numpy/core

  creating build/temp.linux-x86_64-2.7/numpy/core/src

  creating build/temp.linux-x86_64-2.7/numpy/core/src/multiarray

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: numpy/core/src/multiarray/multiarraymodule_onefile.c

  In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:10:0:

  numpy/core/src/multiarray/scalartypes.c.src: In function 鈥榞entype_byteswap鈥?

  numpy/core/src/multiarray/scalartypes.c.src:1205:13: warning: variable 鈥榥umbytes鈥?set but not used [-Wunused-but-set-variable]

           int numbytes;

               ^

  In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:20:0:

  numpy/core/src/multiarray/ctors.c: In function 鈥榑array_from_buffer_3118鈥?

  numpy/core/src/multiarray/ctors.c:1656:15: warning: assignment from incompatible pointer type [enabled by default]

           descr = (PyObject*)_descriptor_from_pep3118_format(view->format);

                 ^

  In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:21:0:

  numpy/core/src/multiarray/iterators.c: In function 鈥榠ter_ass_sub_int鈥?

  numpy/core/src/multiarray/iterators.c:892:20: warning: variable 鈥榯ypecode鈥?set but not used [-Wunused-but-set-variable]

       PyArray_Descr *typecode;

                      ^

  In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:35:0:

  numpy/core/src/multiarray/buffer.c: In function 鈥榑descriptor_from_pep3118_format鈥?

  numpy/core/src/multiarray/buffer.c:771:11: warning: assignment from incompatible pointer type [enabled by default]

       descr = (PyArray_Descr*)PyObject_CallMethod(

             ^

  In file included from numpy/core/src/multiarray/common.c:9:0,

                   from numpy/core/src/multiarray/multiarraymodule_onefile.c:8:

  numpy/core/src/multiarray/multiarraymodule_onefile.c: At top level:

  numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

   simple_capsule_dtor(void *ptr)

   ^

  In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:10:0:

  numpy/core/src/multiarray/scalartypes.c.src:2535:1: warning: 鈥榣onglong_arrtype_hash鈥?defined but not used [-Wunused-function]

   @char@longlong_arrtype_hash(PyObject *obj)

   ^

  In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:13:0:

  numpy/core/src/multiarray/arraytypes.c.src:93:15: warning: 鈥榑SEQUENCE_MESSAGE鈥?defined but not used [-Wunused-variable]

   static char * _SEQUENCE_MESSAGE = "error setting an array element with a sequence";

                 ^

  In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:22:0:

  numpy/core/src/multiarray/mapping.c:74:1: warning: 鈥榑array_ass_item鈥?defined but not used [-Wunused-function]

   _array_ass_item(PyArrayObject *self, Py_ssize_t i, PyObject *v)

   ^

  In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:19:0:

  numpy/core/src/multiarray/flagsobject.c: In function 鈥榓rrayflags_richcompare鈥?

  numpy/core/src/multiarray/flagsobject.c:582:39: warning: 鈥榗mp鈥?may be used uninitialized in this function [-Wmaybe-uninitialized]

           result = (cmp == 0) ? Py_True : Py_False;

                                         ^

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/core/src/multiarray/multiarraymodule_onefile.o -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -o build/lib.linux-x86_64-2.7/numpy/core/multiarray.so

  building 'numpy.core.umath' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7/numpy/core/src/umath

  compile options: '-Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: numpy/core/src/umath/umathmodule_onefile.c

  In file included from numpy/core/src/umath/loops.c.src:17:0,

                   from numpy/core/src/umath/umathmodule_onefile.c:1:

  numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

   simple_capsule_dtor(void *ptr)

   ^

  In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

  numpy/core/src/umath/loops.c.src:1287:1: warning: 鈥楥LONGDOUBLE_logical_and鈥?defined but not used [-Wunused-function]

   C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

   ^

  In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

  numpy/core/src/umath/loops.c.src:1287:1: warning: 鈥楥LONGDOUBLE_logical_or鈥?defined but not used [-Wunused-function]

   C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

   ^

  numpy/core/src/umath/loops.c.src:1300:1: warning: 鈥楥LONGDOUBLE_logical_xor鈥?defined but not used [-Wunused-function]

   C@TYPE@_logical_xor(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

   ^

  numpy/core/src/umath/loops.c.src:1314:1: warning: 鈥楥LONGDOUBLE_logical_not鈥?defined but not used [-Wunused-function]

   C@TYPE@_logical_not(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

   ^

  In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

  numpy/core/src/umath/loops.c.src:1371:1: warning: 鈥楥LONGDOUBLE_ones_like鈥?defined but not used [-Wunused-function]

   C@TYPE@_ones_like(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(data))

   ^

  In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

  numpy/core/src/umath/loops.c.src:1428:1: warning: 鈥楥LONGDOUBLE_maximum鈥?defined but not used [-Wunused-function]

   C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

   ^

  In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

  numpy/core/src/umath/loops.c.src:1428:1: warning: 鈥楥LONGDOUBLE_minimum鈥?defined but not used [-Wunused-function]

   C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

   ^

  In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

  numpy/core/src/umath/loops.c.src:1452:1: warning: 鈥楥LONGDOUBLE_fmax鈥?defined but not used [-Wunused-function]

   C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

   ^

  In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

  numpy/core/src/umath/loops.c.src:1452:1: warning: 鈥楥LONGDOUBLE_fmin鈥?defined but not used [-Wunused-function]

   C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

   ^

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/core/src/umath/umathmodule_onefile.o -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -o build/lib.linux-x86_64-2.7/numpy/core/umath.so

  building 'numpy.core.scalarmath' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/scalarmathmodule.c

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榮longlong_overflow鈥?

  numpy/core/src/scalarmathmodule.c.src:65:40: warning: variable 鈥榸鈥?set but not used [-Wunused-but-set-variable]

       ulonglong ah, al, bh, bl, w, x, y, z;

                                          ^

  numpy/core/src/scalarmathmodule.c.src:65:37: warning: variable 鈥榶鈥?set but not used [-Wunused-but-set-variable]

       ulonglong ah, al, bh, bl, w, x, y, z;

                                       ^

  numpy/core/src/scalarmathmodule.c.src:65:34: warning: variable 鈥榵鈥?set but not used [-Wunused-but-set-variable]

       ulonglong ah, al, bh, bl, w, x, y, z;

                                    ^

  numpy/core/src/scalarmathmodule.c.src:65:31: warning: variable 鈥榳鈥?set but not used [-Wunused-but-set-variable]

       ulonglong ah, al, bh, bl, w, x, y, z;

                                 ^

  numpy/core/src/scalarmathmodule.c.src:64:18: warning: variable 鈥榖鈥?set but not used [-Wunused-but-set-variable]

       ulonglong a, b;

                    ^

  numpy/core/src/scalarmathmodule.c.src:64:15: warning: variable 鈥榓鈥?set but not used [-Wunused-but-set-variable]

       ulonglong a, b;

                 ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榰byte_power鈥?

  numpy/core/src/scalarmathmodule.c.src:778:11: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1=0;

             ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榰short_power鈥?

  numpy/core/src/scalarmathmodule.c.src:778:11: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1=0;

             ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榰int_power鈥?

  numpy/core/src/scalarmathmodule.c.src:778:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1=0;

              ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榰long_power鈥?

  numpy/core/src/scalarmathmodule.c.src:778:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1=0;

              ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榰longlong_power鈥?

  numpy/core/src/scalarmathmodule.c.src:778:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1=0;

              ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榝loat_power鈥?

  numpy/core/src/scalarmathmodule.c.src:778:11: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1=0;

             ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榙ouble_power鈥?

  numpy/core/src/scalarmathmodule.c.src:778:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1=0;

              ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榣ongdouble_power鈥?

  numpy/core/src/scalarmathmodule.c.src:778:16: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1=0;

                  ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榗float_power鈥?

  numpy/core/src/scalarmathmodule.c.src:774:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1;

              ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榗double_power鈥?

  numpy/core/src/scalarmathmodule.c.src:774:13: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1;

               ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榗longdouble_power鈥?

  numpy/core/src/scalarmathmodule.c.src:774:17: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

       @otyp@ out1;

                   ^

  numpy/core/src/scalarmathmodule.c.src: At top level:

  numpy/core/src/scalarmathmodule.c.src:978:1: warning: function declaration isn鈥檛 a prototype [-Wstrict-prototypes]

   emit_complexwarning()

   ^

  numpy/core/src/scalarmathmodule.c.src: In function 鈥榚mit_complexwarning鈥?

  numpy/core/src/scalarmathmodule.c.src:981:9: warning: unused variable 鈥榬et鈥?[-Wunused-variable]

       int ret;

           ^

  In file included from numpy/core/src/scalarmathmodule.c.src:14:0:

  numpy/core/src/scalarmathmodule.c.src: At top level:

  numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

   simple_capsule_dtor(void *ptr)

   ^

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/scalarmathmodule.o -Lbuild/temp.linux-x86_64-2.7 -lm -o build/lib.linux-x86_64-2.7/numpy/core/scalarmath.so

  building 'numpy.core.umath_tests' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/umath

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/umath/umath_tests.c

  In file included from numpy/core/src/umath/umath_tests.c.src:12:0:

  numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

   simple_capsule_dtor(void *ptr)

   ^

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/umath/umath_tests.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/core/umath_tests.so

  building 'numpy.core.multiarray_tests' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/multiarray

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/multiarray/multiarray_tests.c

  In file included from numpy/core/src/multiarray/multiarray_tests.c.src:4:0:

  numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

   simple_capsule_dtor(void *ptr)

   ^

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/multiarray/multiarray_tests.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/core/multiarray_tests.so

  building 'numpy.lib._compiled_base' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7/numpy/lib

  creating build/temp.linux-x86_64-2.7/numpy/lib/src

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: numpy/lib/src/_compiled_base.c

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/lib/src/_compiled_base.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/lib/_compiled_base.so

  building 'numpy.numarray._capi' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7/numpy/numarray

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: numpy/numarray/_capi.c

  In file included from numpy/numarray/_capi.c:5:0:

  numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

   simple_capsule_dtor(void *ptr)

   ^

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/numarray/_capi.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/numarray/_capi.so

  building 'numpy.fft.fftpack_lite' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7/numpy/fft

  compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: numpy/fft/fftpack.c

  x86_64-linux-gnu-gcc: numpy/fft/fftpack_litemodule.c

  x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/fft/fftpack_litemodule.o build/temp.linux-x86_64-2.7/numpy/fft/fftpack.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/fft/fftpack_lite.so

  building 'numpy.linalg.lapack_lite' extension

  compiling C sources

  C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

  

  creating build/temp.linux-x86_64-2.7/numpy/linalg

  compile options: '-DNO_ATLAS_INFO=1 -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

  x86_64-linux-gnu-gcc: numpy/linalg/lapack_litemodule.c

  x86_64-linux-gnu-gcc: numpy/linalg/python_xerbla.c

  /usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/local/Envs/env1/lib -Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so

  /usr/bin/ld: /usr/local/Envs/env1/lib/liblapack.a(dgeev.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC

  /usr/local/Envs/env1/lib/liblapack.a: error adding symbols: Bad value

  collect2: error: ld returned 1 exit status

  /usr/bin/ld: /usr/local/Envs/env1/lib/liblapack.a(dgeev.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC

  /usr/local/Envs/env1/lib/liblapack.a: error adding symbols: Bad value

  collect2: error: ld returned 1 exit status

  error: Command "/usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/local/Envs/env1/lib -Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1

  

  ----------------------------------------

[31m  Failed building wheel for numpy [0m

[?25h  Running setup.py clean for numpy

Failed to build numpy

Installing collected packages: numpy

  Found existing installation: numpy 1.11.1

    Uninstalling numpy-1.11.1:

      Successfully uninstalled numpy-1.11.1

  Running setup.py install for numpy ... [?25l- \ | / - \ | / - \ | / - \ | / - \ | / - \ | / - \ | error

    Complete output from command /usr/local/Envs/env1/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-zMlE9D/numpy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-LdsvD5-record/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/Envs/env1/include/site/python2.7/numpy:

    Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg'

    F2PY Version 1

    blas_opt_info:

    blas_mkl_info:

      libraries mkl,vml,guide not found in /usr/local/Envs/env1/lib

      libraries mkl,vml,guide not found in /usr/local/lib

      libraries mkl,vml,guide not found in /usr/lib

      NOT AVAILABLE

    

    atlas_blas_threads_info:

    Setting PTATLAS=ATLAS

      libraries ptf77blas,ptcblas,atlas not found in /usr/local/Envs/env1/lib

      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

      libraries ptf77blas,ptcblas,atlas not found in /usr/lib

      NOT AVAILABLE

    

    atlas_blas_info:

      libraries f77blas,cblas,atlas not found in /usr/local/Envs/env1/lib

      libraries f77blas,cblas,atlas not found in /usr/local/lib

      libraries f77blas,cblas,atlas not found in /usr/lib

      NOT AVAILABLE

    

    /tmp/pip-build-zMlE9D/numpy/numpy/distutils/system_info.py:1399: 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__)

    blas_info:

      FOUND:

        libraries = ['blas']

        library_dirs = ['/usr/local/Envs/env1/lib']

        language = f77

    

      FOUND:

        libraries = ['blas']

        library_dirs = ['/usr/local/Envs/env1/lib']

        define_macros = [('NO_ATLAS_INFO', 1)]

        language = f77

    

    lapack_opt_info:

    lapack_mkl_info:

    mkl_info:

      libraries mkl,vml,guide not found in /usr/local/Envs/env1/lib

      libraries mkl,vml,guide not found in /usr/local/lib

      libraries mkl,vml,guide not found in /usr/lib

      NOT AVAILABLE

    

      NOT AVAILABLE

    

    atlas_threads_info:

    Setting PTATLAS=ATLAS

      libraries ptf77blas,ptcblas,atlas not found in /usr/local/Envs/env1/lib

      libraries lapack_atlas not found in /usr/local/Envs/env1/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

    numpy.distutils.system_info.atlas_threads_info

      NOT AVAILABLE

    

    atlas_info:

      libraries f77blas,cblas,atlas not found in /usr/local/Envs/env1/lib

      libraries lapack_atlas not found in /usr/local/Envs/env1/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

    numpy.distutils.system_info.atlas_info

      NOT AVAILABLE

    

    /tmp/pip-build-zMlE9D/numpy/numpy/distutils/system_info.py:1306: 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:

      FOUND:

        libraries = ['lapack']

        library_dirs = ['/usr/local/Envs/env1/lib']

        language = f77

    

      FOUND:

        libraries = ['lapack', 'blas']

        library_dirs = ['/usr/local/Envs/env1/lib']

        define_macros = [('NO_ATLAS_INFO', 1)]

        language = f77

    

    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 GnuFCompiler

    Could not locate executable g77

    Could not locate executable f77

    customize IntelFCompiler

    Could not locate executable ifort

    Could not locate executable ifc

    customize LaheyFCompiler

    Could not locate executable lf95

    customize PGroupFCompiler

    Could not locate executable pgf90

    Could not locate executable pgf77

    customize AbsoftFCompiler

    Could not locate executable f90

    customize NAGFCompiler

    Found executable /usr/bin/f95

    customize VastFCompiler

    customize CompaqFCompiler

    Could not locate executable fort

    customize IntelItaniumFCompiler

    Could not locate executable efort

    Could not locate executable efc

    customize IntelEM64TFCompiler

    customize Gnu95FCompiler

    Found executable /usr/bin/gfortran

    customize Gnu95FCompiler

    customize Gnu95FCompiler using config

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    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/include -I/usr/include/python2.7 -c'

    x86_64-linux-gnu-gcc: _configtest.c

    x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest

    success!

    removing: _configtest.c _configtest.o _configtest

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    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/include -I/usr/include/python2.7 -c'

    x86_64-linux-gnu-gcc: _configtest.c

    _configtest.c:1:5: warning: conflicting types for built-in function 鈥榚xp鈥?[enabled by default]

     int exp (void);

         ^

    x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest

    _configtest.o: In function `main':

    /tmp/pip-build-zMlE9D/numpy/_configtest.c:6: undefined reference to `exp'

    collect2: error: ld returned 1 exit status

    _configtest.o: In function `main':

    /tmp/pip-build-zMlE9D/numpy/_configtest.c:6: undefined reference to `exp'

    collect2: error: ld returned 1 exit status

    failure.

    removing: _configtest.c _configtest.o

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    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/include -I/usr/include/python2.7 -c'

    x86_64-linux-gnu-gcc: _configtest.c

    _configtest.c:1:5: warning: conflicting types for built-in function 鈥榚xp鈥?[enabled by default]

     int exp (void);

         ^

    x86_64-linux-gnu-gcc -pthread _configtest.o -lm -o _configtest

    success!

    removing: _configtest.c _configtest.o _configtest

    building extension "numpy.core._sort" sources

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.

    executing numpy/core/code_generators/generate_numpy_api.py

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.

    numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h']

    building extension "numpy.core.multiarray" sources

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.

    executing numpy/core/code_generators/generate_numpy_api.py

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.

    numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h']

    building extension "numpy.core.umath" sources

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.

    executing numpy/core/code_generators/generate_ufunc_api.py

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources.

      adding 'build/src.linux-x86_64-2.7/numpy/core/src/umath' to include_dirs.

    numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/src/umath/funcs.inc', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h']

    building extension "numpy.core.scalarmath" sources

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h' to sources.

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h' to sources.

    executing numpy/core/code_generators/generate_numpy_api.py

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h' to sources.

    executing numpy/core/code_generators/generate_ufunc_api.py

      adding 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h' to sources.

    numpy.core - nothing done with h_files = ['build/src.linux-x86_64-2.7/numpy/core/include/numpy/config.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/_numpyconfig.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h', 'build/src.linux-x86_64-2.7/numpy/core/include/numpy/__ufunc_api.h']

    building extension "numpy.core._dotblas" sources

    building extension "numpy.core.umath_tests" sources

    building extension "numpy.core.multiarray_tests" sources

    building extension "numpy.lib._compiled_base" sources

    building extension "numpy.numarray._capi" sources

    building extension "numpy.fft.fftpack_lite" sources

    building extension "numpy.linalg.lapack_lite" sources

      adding 'numpy/linalg/lapack_litemodule.c' to sources.

      adding 'numpy/linalg/python_xerbla.c' to sources.

    building extension "numpy.random.mtrand" sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    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/include -I/usr/include/python2.7 -c'

    x86_64-linux-gnu-gcc: _configtest.c

    x86_64-linux-gnu-gcc -pthread _configtest.o -o _configtest

    _configtest

    failure.

    removing: _configtest.c _configtest.o _configtest

    building data_files sources

    build_src: building npy-pkg config files

    running build_py

    creating build/lib.linux-x86_64-2.7

    creating build/lib.linux-x86_64-2.7/numpy

    copying numpy/__init__.py -> build/lib.linux-x86_64-2.7/numpy

    copying numpy/_import_tools.py -> build/lib.linux-x86_64-2.7/numpy

    copying numpy/setupscons.py -> build/lib.linux-x86_64-2.7/numpy

    copying numpy/matlib.py -> build/lib.linux-x86_64-2.7/numpy

    copying numpy/version.py -> build/lib.linux-x86_64-2.7/numpy

    copying numpy/dual.py -> build/lib.linux-x86_64-2.7/numpy

    copying numpy/setup.py -> build/lib.linux-x86_64-2.7/numpy

    copying numpy/add_newdocs.py -> build/lib.linux-x86_64-2.7/numpy

    copying numpy/ctypeslib.py -> build/lib.linux-x86_64-2.7/numpy

    copying build/src.linux-x86_64-2.7/numpy/__config__.py -> build/lib.linux-x86_64-2.7/numpy

    creating build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/core.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/__init__.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/ccompiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/environment.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/system_info.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/log.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/exec_command.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/__version__.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/compat.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/mingw32ccompiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/intelccompiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/from_template.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/extension.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/interactive.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/lib2def.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/line_endings.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/conv_template.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/setup.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/cpuinfo.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/misc_util.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/unixccompiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/info.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/numpy_distribution.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying numpy/distutils/npy_pkg_config.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    copying build/src.linux-x86_64-2.7/numpy/distutils/__config__.py -> build/lib.linux-x86_64-2.7/numpy/distutils

    creating build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/__init__.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/install_data.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/egg_info.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/install.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/build.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/build_clib.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/build_ext.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/scons.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/build_scripts.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/config_compiler.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/install_headers.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/config.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/sdist.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/build_py.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/autodist.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/develop.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/install_clib.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/bdist_rpm.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    copying numpy/distutils/command/build_src.py -> build/lib.linux-x86_64-2.7/numpy/distutils/command

    creating build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/__init__.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/vast.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/g95.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/none.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/hpux.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/ibm.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/absoft.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/intel.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/sun.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/compaq.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/mips.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/lahey.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/pg.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/gnu.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    copying numpy/distutils/fcompiler/nag.py -> build/lib.linux-x86_64-2.7/numpy/distutils/fcompiler

    creating build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/__init__.py -> build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/nosetester.py -> build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/utils.py -> build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/noseclasses.py -> build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/nulltester.py -> build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/setup.py -> build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/decorators.py -> build/lib.linux-x86_64-2.7/numpy/testing

    copying numpy/testing/numpytest.py -> build/lib.linux-x86_64-2.7/numpy/testing

    creating build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/f90mod_rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/__init__.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/cfuncs.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/__version__.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/f2py_testing.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/func2subr.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/diagnose.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/cb_rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/common_rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/auxfuncs.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/capi_maps.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/setup.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/crackfortran.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/info.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/use_rules.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    copying numpy/f2py/f2py2e.py -> build/lib.linux-x86_64-2.7/numpy/f2py

    creating build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/numerictypes.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/machar.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/records.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/__init__.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/scons_support.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/numeric.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/setup_common.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/shape_base.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/fromnumeric.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/_mx_datetime_parser.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/_internal.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/function_base.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/setup.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/defchararray.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/memmap.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/getlimits.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/arrayprint.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/info.py -> build/lib.linux-x86_64-2.7/numpy/core

    copying numpy/core/code_generators/generate_numpy_api.py -> build/lib.linux-x86_64-2.7/numpy/core

    creating build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/financial.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/user_array.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/ufunclike.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/__init__.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/recfunctions.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/arrayterator.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/_datasource.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/scimath.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/utils.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/shape_base.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/stride_tricks.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/format.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/npyio.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/function_base.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/twodim_base.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/index_tricks.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/setup.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/type_check.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/arraysetops.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/_iotools.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/info.py -> build/lib.linux-x86_64-2.7/numpy/lib

    copying numpy/lib/polynomial.py -> build/lib.linux-x86_64-2.7/numpy/lib

    creating build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/ufuncs.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/user_array.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/__init__.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/linear_algebra.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/rng_stats.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/fix_default_axis.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/alter_code2.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/alter_code1.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/array_printer.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/matrix.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/compat.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/arrayfns.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/fft.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/functions.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/typeconv.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/setup.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/misc.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/precision.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/rng.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/ma.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/random_array.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    copying numpy/oldnumeric/mlab.py -> build/lib.linux-x86_64-2.7/numpy/oldnumeric

    creating build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/numerictypes.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/ufuncs.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/__init__.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/linear_algebra.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/nd_image.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/alter_code2.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/alter_code1.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/session.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/matrix.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/util.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/compat.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/fft.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/functions.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/setup.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/convolve.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/ma.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/random_array.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/image.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    copying numpy/numarray/mlab.py -> build/lib.linux-x86_64-2.7/numpy/numarray

    creating build/lib.linux-x86_64-2.7/numpy/fft

    copying numpy/fft/__init__.py -> build/lib.linux-x86_64-2.7/numpy/fft

    copying numpy/fft/fftpack.py -> build/lib.linux-x86_64-2.7/numpy/fft

    copying numpy/fft/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/fft

    copying numpy/fft/helper.py -> build/lib.linux-x86_64-2.7/numpy/fft

    copying numpy/fft/setup.py -> build/lib.linux-x86_64-2.7/numpy/fft

    copying numpy/fft/info.py -> build/lib.linux-x86_64-2.7/numpy/fft

    creating build/lib.linux-x86_64-2.7/numpy/linalg

    copying numpy/linalg/__init__.py -> build/lib.linux-x86_64-2.7/numpy/linalg

    copying numpy/linalg/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/linalg

    copying numpy/linalg/linalg.py -> build/lib.linux-x86_64-2.7/numpy/linalg

    copying numpy/linalg/setup.py -> build/lib.linux-x86_64-2.7/numpy/linalg

    copying numpy/linalg/info.py -> build/lib.linux-x86_64-2.7/numpy/linalg

    creating build/lib.linux-x86_64-2.7/numpy/random

    copying numpy/random/__init__.py -> build/lib.linux-x86_64-2.7/numpy/random

    copying numpy/random/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/random

    copying numpy/random/setup.py -> build/lib.linux-x86_64-2.7/numpy/random

    copying numpy/random/info.py -> build/lib.linux-x86_64-2.7/numpy/random

    creating build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/core.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/mrecords.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/__init__.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/testutils.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/timer_comparison.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/bench.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/extras.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/version.py -> build/lib.linux-x86_64-2.7/numpy/ma

    copying numpy/ma/setup.py -> build/lib.linux-x86_64-2.7/numpy/ma

    creating build/lib.linux-x86_64-2.7/numpy/matrixlib

    copying numpy/matrixlib/__init__.py -> build/lib.linux-x86_64-2.7/numpy/matrixlib

    copying numpy/matrixlib/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/matrixlib

    copying numpy/matrixlib/setup.py -> build/lib.linux-x86_64-2.7/numpy/matrixlib

    copying numpy/matrixlib/defmatrix.py -> build/lib.linux-x86_64-2.7/numpy/matrixlib

    creating build/lib.linux-x86_64-2.7/numpy/compat

    copying numpy/compat/__init__.py -> build/lib.linux-x86_64-2.7/numpy/compat

    copying numpy/compat/setupscons.py -> build/lib.linux-x86_64-2.7/numpy/compat

    copying numpy/compat/py3k.py -> build/lib.linux-x86_64-2.7/numpy/compat

    copying numpy/compat/_inspect.py -> build/lib.linux-x86_64-2.7/numpy/compat

    copying numpy/compat/setup.py -> build/lib.linux-x86_64-2.7/numpy/compat

    creating build/lib.linux-x86_64-2.7/numpy/polynomial

    copying numpy/polynomial/__init__.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

    copying numpy/polynomial/polytemplate.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

    copying numpy/polynomial/polyutils.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

    copying numpy/polynomial/chebyshev.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

    copying numpy/polynomial/setup.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

    copying numpy/polynomial/polynomial.py -> build/lib.linux-x86_64-2.7/numpy/polynomial

    creating build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/basics.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/ufuncs.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/__init__.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/internals.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/subclassing.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/methods_vs_functions.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/byteswapping.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/structured_arrays.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/howtofind.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/creation.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/misc.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/jargon.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/performance.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/indexing.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/broadcasting.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/glossary.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/io.py -> build/lib.linux-x86_64-2.7/numpy/doc

    copying numpy/doc/constants.py -> build/lib.linux-x86_64-2.7/numpy/doc

    running build_clib

    customize UnixCCompiler

    customize UnixCCompiler using build_clib

    building 'npymath' library

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7

    creating build/temp.linux-x86_64-2.7/build

    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7

    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy

    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core

    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src

    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/npymath

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/ieee754.c

    x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math.c

    x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/npymath/npy_math_complex.c

    ar: adding 3 object files to build/temp.linux-x86_64-2.7/libnpymath.a

    running build_ext

    customize UnixCCompiler

    customize UnixCCompiler using build_ext

    customize GnuFCompiler

    customize IntelFCompiler

    customize LaheyFCompiler

    customize PGroupFCompiler

    customize AbsoftFCompiler

    customize NAGFCompiler

    customize VastFCompiler

    customize CompaqFCompiler

    customize IntelItaniumFCompiler

    customize IntelEM64TFCompiler

    customize Gnu95FCompiler

    customize Gnu95FCompiler

    customize Gnu95FCompiler using build_ext

    building 'numpy.core._sort' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.c

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/_sortmodule.o -Lbuild/temp.linux-x86_64-2.7 -lm -o build/lib.linux-x86_64-2.7/numpy/core/_sort.so

    building 'numpy.core.multiarray' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7/numpy

    creating build/temp.linux-x86_64-2.7/numpy/core

    creating build/temp.linux-x86_64-2.7/numpy/core/src

    creating build/temp.linux-x86_64-2.7/numpy/core/src/multiarray

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: numpy/core/src/multiarray/multiarraymodule_onefile.c

    In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:10:0:

    numpy/core/src/multiarray/scalartypes.c.src: In function 鈥榞entype_byteswap鈥?

    numpy/core/src/multiarray/scalartypes.c.src:1205:13: warning: variable 鈥榥umbytes鈥?set but not used [-Wunused-but-set-variable]

             int numbytes;

                 ^

    In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:20:0:

    numpy/core/src/multiarray/ctors.c: In function 鈥榑array_from_buffer_3118鈥?

    numpy/core/src/multiarray/ctors.c:1656:15: warning: assignment from incompatible pointer type [enabled by default]

             descr = (PyObject*)_descriptor_from_pep3118_format(view->format);

                   ^

    In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:21:0:

    numpy/core/src/multiarray/iterators.c: In function 鈥榠ter_ass_sub_int鈥?

    numpy/core/src/multiarray/iterators.c:892:20: warning: variable 鈥榯ypecode鈥?set but not used [-Wunused-but-set-variable]

         PyArray_Descr *typecode;

                        ^

    In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:35:0:

    numpy/core/src/multiarray/buffer.c: In function 鈥榑descriptor_from_pep3118_format鈥?

    numpy/core/src/multiarray/buffer.c:771:11: warning: assignment from incompatible pointer type [enabled by default]

         descr = (PyArray_Descr*)PyObject_CallMethod(

               ^

    In file included from numpy/core/src/multiarray/common.c:9:0,

                     from numpy/core/src/multiarray/multiarraymodule_onefile.c:8:

    numpy/core/src/multiarray/multiarraymodule_onefile.c: At top level:

    numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

     simple_capsule_dtor(void *ptr)

     ^

    In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:10:0:

    numpy/core/src/multiarray/scalartypes.c.src:2535:1: warning: 鈥榣onglong_arrtype_hash鈥?defined but not used [-Wunused-function]

     @char@longlong_arrtype_hash(PyObject *obj)

     ^

    In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:13:0:

    numpy/core/src/multiarray/arraytypes.c.src:93:15: warning: 鈥榑SEQUENCE_MESSAGE鈥?defined but not used [-Wunused-variable]

     static char * _SEQUENCE_MESSAGE = "error setting an array element with a sequence";

                   ^

    In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:22:0:

    numpy/core/src/multiarray/mapping.c:74:1: warning: 鈥榑array_ass_item鈥?defined but not used [-Wunused-function]

     _array_ass_item(PyArrayObject *self, Py_ssize_t i, PyObject *v)

     ^

    In file included from numpy/core/src/multiarray/multiarraymodule_onefile.c:19:0:

    numpy/core/src/multiarray/flagsobject.c: In function 鈥榓rrayflags_richcompare鈥?

    numpy/core/src/multiarray/flagsobject.c:582:39: warning: 鈥榗mp鈥?may be used uninitialized in this function [-Wmaybe-uninitialized]

             result = (cmp == 0) ? Py_True : Py_False;

                                           ^

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/core/src/multiarray/multiarraymodule_onefile.o -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -o build/lib.linux-x86_64-2.7/numpy/core/multiarray.so

    building 'numpy.core.umath' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7/numpy/core/src/umath

    compile options: '-Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: numpy/core/src/umath/umathmodule_onefile.c

    In file included from numpy/core/src/umath/loops.c.src:17:0,

                     from numpy/core/src/umath/umathmodule_onefile.c:1:

    numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

     simple_capsule_dtor(void *ptr)

     ^

    In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

    numpy/core/src/umath/loops.c.src:1287:1: warning: 鈥楥LONGDOUBLE_logical_and鈥?defined but not used [-Wunused-function]

     C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

     ^

    In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

    numpy/core/src/umath/loops.c.src:1287:1: warning: 鈥楥LONGDOUBLE_logical_or鈥?defined but not used [-Wunused-function]

     C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

     ^

    numpy/core/src/umath/loops.c.src:1300:1: warning: 鈥楥LONGDOUBLE_logical_xor鈥?defined but not used [-Wunused-function]

     C@TYPE@_logical_xor(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

     ^

    numpy/core/src/umath/loops.c.src:1314:1: warning: 鈥楥LONGDOUBLE_logical_not鈥?defined but not used [-Wunused-function]

     C@TYPE@_logical_not(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

     ^

    In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

    numpy/core/src/umath/loops.c.src:1371:1: warning: 鈥楥LONGDOUBLE_ones_like鈥?defined but not used [-Wunused-function]

     C@TYPE@_ones_like(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(data))

     ^

    In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

    numpy/core/src/umath/loops.c.src:1428:1: warning: 鈥楥LONGDOUBLE_maximum鈥?defined but not used [-Wunused-function]

     C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

     ^

    In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

    numpy/core/src/umath/loops.c.src:1428:1: warning: 鈥楥LONGDOUBLE_minimum鈥?defined but not used [-Wunused-function]

     C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

     ^

    In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

    numpy/core/src/umath/loops.c.src:1452:1: warning: 鈥楥LONGDOUBLE_fmax鈥?defined but not used [-Wunused-function]

     C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

     ^

    In file included from numpy/core/src/umath/umathmodule_onefile.c:1:0:

    numpy/core/src/umath/loops.c.src:1452:1: warning: 鈥楥LONGDOUBLE_fmin鈥?defined but not used [-Wunused-function]

     C@TYPE@_@kind@(char **args, intp *dimensions, intp *steps, void *NPY_UNUSED(func))

     ^

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/core/src/umath/umathmodule_onefile.o -Lbuild/temp.linux-x86_64-2.7 -lnpymath -lm -o build/lib.linux-x86_64-2.7/numpy/core/umath.so

    building 'numpy.core.scalarmath' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/scalarmathmodule.c

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榮longlong_overflow鈥?

    numpy/core/src/scalarmathmodule.c.src:65:40: warning: variable 鈥榸鈥?set but not used [-Wunused-but-set-variable]

         ulonglong ah, al, bh, bl, w, x, y, z;

                                            ^

    numpy/core/src/scalarmathmodule.c.src:65:37: warning: variable 鈥榶鈥?set but not used [-Wunused-but-set-variable]

         ulonglong ah, al, bh, bl, w, x, y, z;

                                         ^

    numpy/core/src/scalarmathmodule.c.src:65:34: warning: variable 鈥榵鈥?set but not used [-Wunused-but-set-variable]

         ulonglong ah, al, bh, bl, w, x, y, z;

                                      ^

    numpy/core/src/scalarmathmodule.c.src:65:31: warning: variable 鈥榳鈥?set but not used [-Wunused-but-set-variable]

         ulonglong ah, al, bh, bl, w, x, y, z;

                                   ^

    numpy/core/src/scalarmathmodule.c.src:64:18: warning: variable 鈥榖鈥?set but not used [-Wunused-but-set-variable]

         ulonglong a, b;

                      ^

    numpy/core/src/scalarmathmodule.c.src:64:15: warning: variable 鈥榓鈥?set but not used [-Wunused-but-set-variable]

         ulonglong a, b;

                   ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榰byte_power鈥?

    numpy/core/src/scalarmathmodule.c.src:778:11: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1=0;

               ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榰short_power鈥?

    numpy/core/src/scalarmathmodule.c.src:778:11: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1=0;

               ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榰int_power鈥?

    numpy/core/src/scalarmathmodule.c.src:778:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1=0;

                ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榰long_power鈥?

    numpy/core/src/scalarmathmodule.c.src:778:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1=0;

                ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榰longlong_power鈥?

    numpy/core/src/scalarmathmodule.c.src:778:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1=0;

                ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榝loat_power鈥?

    numpy/core/src/scalarmathmodule.c.src:778:11: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1=0;

               ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榙ouble_power鈥?

    numpy/core/src/scalarmathmodule.c.src:778:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1=0;

                ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榣ongdouble_power鈥?

    numpy/core/src/scalarmathmodule.c.src:778:16: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1=0;

                    ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榗float_power鈥?

    numpy/core/src/scalarmathmodule.c.src:774:12: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1;

                ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榗double_power鈥?

    numpy/core/src/scalarmathmodule.c.src:774:13: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1;

                 ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榗longdouble_power鈥?

    numpy/core/src/scalarmathmodule.c.src:774:17: warning: variable 鈥榦ut1鈥?set but not used [-Wunused-but-set-variable]

         @otyp@ out1;

                     ^

    numpy/core/src/scalarmathmodule.c.src: At top level:

    numpy/core/src/scalarmathmodule.c.src:978:1: warning: function declaration isn鈥檛 a prototype [-Wstrict-prototypes]

     emit_complexwarning()

     ^

    numpy/core/src/scalarmathmodule.c.src: In function 鈥榚mit_complexwarning鈥?

    numpy/core/src/scalarmathmodule.c.src:981:9: warning: unused variable 鈥榬et鈥?[-Wunused-variable]

         int ret;

             ^

    In file included from numpy/core/src/scalarmathmodule.c.src:14:0:

    numpy/core/src/scalarmathmodule.c.src: At top level:

    numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

     simple_capsule_dtor(void *ptr)

     ^

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/scalarmathmodule.o -Lbuild/temp.linux-x86_64-2.7 -lm -o build/lib.linux-x86_64-2.7/numpy/core/scalarmath.so

    building 'numpy.core.umath_tests' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/umath

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/umath/umath_tests.c

    In file included from numpy/core/src/umath/umath_tests.c.src:12:0:

    numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

     simple_capsule_dtor(void *ptr)

     ^

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/umath/umath_tests.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/core/umath_tests.so

    building 'numpy.core.multiarray_tests' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/multiarray

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: build/src.linux-x86_64-2.7/numpy/core/src/multiarray/multiarray_tests.c

    In file included from numpy/core/src/multiarray/multiarray_tests.c.src:4:0:

    numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

     simple_capsule_dtor(void *ptr)

     ^

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/build/src.linux-x86_64-2.7/numpy/core/src/multiarray/multiarray_tests.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/core/multiarray_tests.so

    building 'numpy.lib._compiled_base' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7/numpy/lib

    creating build/temp.linux-x86_64-2.7/numpy/lib/src

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: numpy/lib/src/_compiled_base.c

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/lib/src/_compiled_base.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/lib/_compiled_base.so

    building 'numpy.numarray._capi' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7/numpy/numarray

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: numpy/numarray/_capi.c

    In file included from numpy/numarray/_capi.c:5:0:

    numpy/core/include/numpy/npy_3kcompat.h:391:1: warning: 鈥榮imple_capsule_dtor鈥?defined but not used [-Wunused-function]

     simple_capsule_dtor(void *ptr)

     ^

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/numarray/_capi.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/numarray/_capi.so

    building 'numpy.fft.fftpack_lite' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7/numpy/fft

    compile options: '-Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: numpy/fft/fftpack.c

    x86_64-linux-gnu-gcc: numpy/fft/fftpack_litemodule.c

    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -D_FORTIFY_SOURCE=2 -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security build/temp.linux-x86_64-2.7/numpy/fft/fftpack_litemodule.o build/temp.linux-x86_64-2.7/numpy/fft/fftpack.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/fft/fftpack_lite.so

    building 'numpy.linalg.lapack_lite' extension

    compiling C sources

    C compiler: x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC

    

    creating build/temp.linux-x86_64-2.7/numpy/linalg

    compile options: '-DNO_ATLAS_INFO=1 -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/usr/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/multiarray -Ibuild/src.linux-x86_64-2.7/numpy/core/src/umath -c'

    x86_64-linux-gnu-gcc: numpy/linalg/lapack_litemodule.c

    x86_64-linux-gnu-gcc: numpy/linalg/python_xerbla.c

    /usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/local/Envs/env1/lib -Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so

    /usr/bin/ld: /usr/local/Envs/env1/lib/liblapack.a(dgeev.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC

    /usr/local/Envs/env1/lib/liblapack.a: error adding symbols: Bad value

    collect2: error: ld returned 1 exit status

    /usr/bin/ld: /usr/local/Envs/env1/lib/liblapack.a(dgeev.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC

    /usr/local/Envs/env1/lib/liblapack.a: error adding symbols: Bad value

    collect2: error: ld returned 1 exit status

    error: Command "/usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/usr/local/Envs/env1/lib -Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1

    

    ----------------------------------------

[?25h  Rolling back uninstall of numpy

[31mCommand "/usr/local/Envs/env1/bin/python -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-zMlE9D/numpy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-LdsvD5-record/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/Envs/env1/include/site/python2.7/numpy" failed with error code 1 in /tmp/pip-build-zMlE9D/numpy/ [0m

(env1) ]0;jiaxu@neerjalinux4: ~ jiaxu@neerjalinux4:~$  

[clair...@gmail.com]

I'm sorry that the numpy  installation output is very long. So I put it in the attached file. 

BTW, I''ve sudo cp the libraries of blas, cblas, lapack and atlas to the "/usr/local/Envs/env1/lib" and "/usr/local/lib".

On Wednesday, 27 July 2016 00:25:00 UTC+8, Ali Faruqi wrote:

[Ali Ahmad Faruqi]

Hi Jia,

It most definitely seems like a compiler issue to me. Unfortunately, I do not have access to a Linux system these days, so I can't explore further. Googling further, I found a post on Stack Overflow discussing a similar problem and a possible solution. 

If this doesn't help, my best bet would be look into the user group discussion of NumPy to figure out more. 

Maybe the PICRUSt developers have some insight to offer. Thanks and sorry for not being able to help much here.

Best,

Ali

[Ali Ahmad Faruqi]

Hi Jia,

Please refer to my reply to Kassi on this thread on July 24, 2016. It has new notes on installing. For PyCogent, you can do a pip install now:

pip install cogent==1.5.3

Thanks,

Ali

On Mon, Aug 1, 2016 at 2:06 AM, <clair...@gmail.com> wrote:

Hi Ali,

Thank you for your suggestion. And I've successfully installed the right version of BIOM. But another problem came out. That is the install of Pycogent.

When I run as you shared:

# PyCogent for PICRUSt
wget http://pycogent.org/_downloads/cogent-requirements.txt
DONT_USE_PYREX=1 pip install -r cogent-requirements.txt 

the warning message:

--2016-08-01 16:49:22--  http://pycogent.org/_downloads/cogent-requirements.txt

Resolving pycogent.org (pycogent.org)... 192.30.252.153, 192.30.252.154

Connecting to pycogent.org (pycogent.org)|192.30.252.153|:80... connected.

HTTP request sent, awaiting response... 404 Not Found

2016-08-01 16:49:23 ERROR 404: Not Found.

It seems "cogent-requirements.txt" has already been removed. Although I also tried to download this version and installed it manually, the installation failed. Would you please kindly send me this file?  

Best,

Jia

在 2016年7月27日星期三 UTC+8上午11:38:20，Ali Faruqi写道：

[Michael]

Hi Good day! i am installing picrust on qiime as describe in this thread using the latest version of picrust 1.1.1 and its dependencies. However when I run the command  print_picrust_config.py i got the following erroe below (highlighted in red color font).

(env1) qiime@qiime-190-virtual-box:~/biom-format-2.1.5/picrust-1.1.1$ print_picrust_config.py

System information

==================

          Platform: linux2

Python/GCC version: 2.7.3 (default, Dec 18 2014, 19:10:20)  [GCC 4.6.3]

 Python executable: /usr/bin/python

Dependency versions

===================

         NumPy version: 1.9.2

   biom-format version: ERROR: Can't find the BIOM library code (or numpy) - is it installed and in your $PYTHONPATH?

      PyCogent version: 1.5.3

       PICRUSt version: 1.1.1

PICRUSt script version: 1.1.1

--------------

when i check if numpy is install, it said  'Requirement already satisfied: numpy in /usr/local/Envs/env1/lib/python2.7/site-packages.'. But the version i installed was numpy (version 1.12.1).

Should i installed numpy version 1.9.2 to satisfy the depency requirement or use the latest version?

Thank you in advance.

[Gavin Douglas]

Hey Michael,

I think numpy v1.9.2 should also work fine, however I think the problem might be that biom-format isn’t installed correctly. Did you install biom-format using pip?

Best,

Gavin

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[Michael]

Hi Gavin. Yes. I installed the numpy using this command

pip install numpy==1.12.1

[Michael]

here is the full command i used to install Picrust as suggested in this thread.

## virtualenv for PICRUSt

sudo pip install virtualenvwrapper

sudo mkdir /usr/local/Envs/

sudo chmod -R 777 /usr/local/Envs/

export WORKON_HOME=/usr/local/Envs/

mkdir -p $WORKON_HOME

sudo cp /usr/local/bin/virtualenvwrapper.sh /etc/profile.d/

source /etc/profile.d/virtualenvwrapper.sh

mkvirtualenv env1

pip install numpy==1.12.1

pip install pyqi 

pip install h5py 

## BIOM for PICRUSt

wget https://pypi.python.org/packages/source/b/biom-format/biom-format-2.1.5.tar.gz

tar -xvzf biom-format-2.1.5.tar.gz

sudo mv biom-format-1.3.1.tar.gz biom-format-2.1.5

cd biom-format-2.1.5/ 

sudo python setup.py build

sudo python setup.py install 

##PyCogent for PICRUSt

pip install cogent==1.5.3

## PICRUSt (1.1.1):

wget https://github.com/picrust/picrust/releases/download/1.1.1/picrust-1.1.1.tar.gz (**if not working see instruction below:)

tar -xzf picrust-1.1.1.tar.gz

mv picrust-1.1.1.tar.gz picrust-1.1.1

wget ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/16S_13_5_precalculated.tab.gz

wget ftp://ftp.microbio.me/pub/picrust-references/picrust-1.0.0/ko_13_5_precalculated.tab.gz

mkdir picrust-1.1.1/picrust/data

sudo mv ko_13_5_precalculated.tab.gz picrust-1.1.1/picrust/data

sudo mv 16S_13_5_precalculated.tab.gz picrust-1.1.1/picrust/data

cd picrust-1.1.1/

sudo python ./setup.py install

print_picrust_config.py 

[Gavin Douglas]

Hi Michael,

PICRUSt is no longer dependent on the older version of biom, which is what this thread was discussing. You should now be able to install PICRUSt using the instructions on the website: https://picrust.github.io/picrust/install.html

If you want to install the required packages in a different environment you could definitely still use virtualenv although anaconda is a more popular choice.

Cheers,

Gavin

[Michael]

Hi Gavin. Thank you for the reply. This means that I can install Picrust directly as per instructions on the website? I read some threads which state that I have to change the biom-format into the older version.

Ill give it a try then. Thank you very much. 

[Gavin Douglas]

Hey Michael,

Yes that’s right. The previous instructions would have worked as well except you will need a new environment if you want to have multiple versions of the same python package.

Cheers,

Gavin

On May 24, 2017, at 11:49 AM, Michael <mln...@up.edu.ph> wrote:

Hi Gavin. Thank you for the reply. This means that I can install Picrust directly as per instructions on the website? I read some threads which state that I have to change the biom-format into the older version.

Ill give it a try then. Thank you very much. 

[Michael]

Hi Gavin. i still get the same error as above 

System information

==================

          Platform: linux2

Python/GCC version: 2.7.3 (default, Dec 18 2014, 19:10:20)  [GCC 4.6.3]

 Python executable: /usr/bin/python

Dependency versions

===================

         NumPy version: 1.9.2

   biom-format version: ERROR: Can't find the BIOM library code (or numpy) - is it installed and in your $PYTHONPATH?

      PyCogent version: 1.5.3

       PICRUSt version: 1.1.1

PICRUSt script version: 1.1.1

--------------

How can i install the correct biom format correctly (biom (version 2.1.5)?

)? 

[Gavin Douglas]

Hi Michael,

There are a few ways you could install it, including by source like you were doing before.

The easiest way is with pip though like this:

pip install biom-format==2.1.5

I haven’t tested the newest biom version out, but that likely will work fine with PICRUSt as well (so you could just type "pip install biom-format”).

Gavin