Numpy is installed, but can't find lapack/blas
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Galen Seilis
Jul 28, 2015, 7:35:11 PM7/28/15
to Qiime Forum
To whom it may concern,
I am trying out the QIIME tutorial on a Linux Mint distro and I have run into an error I would like advice in troubleshooting.
sudo apt-get install numpy
pip install qiime
Requirement already satisfied (use --upgrade to upgrade): qiime in /usr/local/lib/python2.7/dist-packages
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.9.0 in /usr/local/lib/python2.7/dist-packages (from qiime)
Downloading/unpacking scipy>=0.14.0 (from qiime)
Downloading scipy-0.16.0.tar.gz (18.1MB): 18.1MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/scipy/setup.py) egg_info for package scipy
warning: no previously-included files matching '*_subr_*.f' found under directory 'scipy/linalg/src/id_dist/src'
no previously-included directories found matching 'benchmarks/env'
no previously-included directories found matching 'benchmarks/results'
no previously-included directories found matching 'benchmarks/html'
no previously-included directories found matching 'benchmarks/scipy'
no previously-included directories found matching 'scipy/special/tests/data/boost'
no previously-included directories found matching 'scipy/special/tests/data/gsl'
no previously-included directories found matching 'doc/build'
no previously-included directories found matching 'doc/source/generated'
no previously-included directories found matching '*/__pycache__'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.bak' found anywhere in distribution
warning: no previously-included files matching '*.swp' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
Downloading/unpacking cogent==1.5.3 (from qiime)
Downloading cogent-1.5.3.tgz (3.4MB): 3.4MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/cogent/setup.py) egg_info for package cogent
Downloading/unpacking natsort<4.0.0 (from qiime)
Downloading natsort-3.5.6-py2.py3-none-any.whl
Downloading/unpacking matplotlib>=1.1.0,!=1.4.2 (from qiime)
Downloading matplotlib-1.4.3.tar.gz (50.4MB): 50.4MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/matplotlib/setup.py) egg_info for package matplotlib
============================================================================
Edit setup.cfg to change the build options
BUILDING MATPLOTLIB
matplotlib: yes [1.4.3]
python: yes [2.7.6 (default, Jun 22 2015, 17:58:13) [GCC
4.8.2]]
platform: yes [linux2]
REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.9.2]
six: yes [using six version 1.5.2]
dateutil: yes [using dateutil version 1.5]
pytz: yes [using pytz version 2012c]
tornado: yes [using tornado version 3.1.1]
pyparsing: yes [using pyparsing version 2.0.1]
pycxx: yes [Couldn't import. Using local copy.]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
freetype: yes [version 2.5.2]
png: yes [version 1.2.50]
qhull: yes [pkg-config information for 'qhull' could not be
found. Using local copy.]
OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
tests: yes [using nose version 1.3.7 / mock is required to
run the matplotlib test suite. pip/easy_install may
attempt to install it after matplotlib.]
toolkits_tests: yes [using nose version 1.3.7 / mock is required to
run the matplotlib test suite. pip/easy_install may
attempt to install it after matplotlib.]
OPTIONAL BACKEND EXTENSIONS
macosx: no [Mac OS-X only]
qt5agg: no [PyQt5 not found]
qt4agg: yes [installing, Qt: 4.8.6, PyQt: 4.8.6]
pyside: no [PySide not found]
** (-c:16889): WARNING **: Error retrieving accessibility bus address: org.freedesktop.DBus.Error.ServiceUnknown: The name org.a11y.Bus was not provided by any .service files
gtk3agg: yes [installing, version 3.8.10]
** (-c:16900): WARNING **: Error retrieving accessibility bus address: org.freedesktop.DBus.Error.ServiceUnknown: The name org.a11y.Bus was not provided by any .service files
gtk3cairo: yes [installing, version 3.8.10]
gtkagg: no [The C/C++ header for gtk (gtk/gtk.h) could not
be found. You may need to install the development
package.]
tkagg: no [The C/C++ header for Tk (tk.h) could not be
found. You may need to install the development
package.]
wxagg: no [requires wxPython]
gtk: no [The C/C++ header for gtk (gtk/gtk.h) could not
be found. You may need to install the development
package.]
agg: yes [installing]
cairo: yes [installing, pycairo version 1.8.8]
windowing: no [Microsoft Windows only]
OPTIONAL LATEX DEPENDENCIES
dvipng: no
ghostscript: yes [version 9.10]
latex: yes [version 3.1415926]
pdftops: yes [version 0.24.5]
Downloading/unpacking pynast==1.2.2 (from qiime)
Downloading pynast-1.2.2.tar.gz (57kB): 57kB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/pynast/setup.py) egg_info for package pynast
Downloading/unpacking qcli>=0.1.1,<0.2.0 (from qiime)
Downloading qcli-0.1.1.tar.gz
Running setup.py (path:/tmp/pip_build_bioinfo/qcli/setup.py) egg_info for package qcli
Downloading/unpacking gdata (from qiime)
Downloading gdata-2.0.18.tar.gz (2.5MB): 2.5MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/gdata/setup.py) egg_info for package gdata
Downloading/unpacking biom-format>=2.1.4,<2.2.0 (from qiime)
Downloading biom-format-2.1.4.tar.gz (435kB): 435kB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/biom-format/setup.py) egg_info for package biom-format
no previously-included directories found matching 'docs/_build'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
Requirement already satisfied (use --upgrade to upgrade): emperor>=0.9.51,<1.0.0 in /usr/local/lib/python2.7/dist-packages (from qiime)
Requirement already satisfied (use --upgrade to upgrade): scikit-bio>=0.2.3,<0.3.0 in /usr/local/lib/python2.7/dist-packages (from qiime)
Downloading/unpacking burrito-fillings>=0.1.1,<0.2.0 (from qiime)
Downloading burrito-fillings-0.1.1.tar.gz (214kB): 214kB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/burrito-fillings/setup.py) egg_info for package burrito-fillings
Downloading/unpacking pandas>=0.13.1 (from qiime)
Downloading pandas-0.16.2.tar.gz (4.9MB): 4.9MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/pandas/setup.py) egg_info for package pandas
warning: no files found matching 'README.rst'
no previously-included directories found matching 'doc/build'
warning: no directories found matching 'examples'
warning: no previously-included files matching '*.so' found anywhere in distribution
warning: no previously-included files matching '*.pyd' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '#*' found anywhere in distribution
warning: no previously-included files matching '.git*' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no previously-included files matching '*.png' found anywhere in distribution
Downloading/unpacking burrito>=0.9.1,<1.0.0 (from qiime)
Downloading burrito-0.9.1.tar.gz
Running setup.py (path:/tmp/pip_build_bioinfo/burrito/setup.py) egg_info for package burrito
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
Downloading/unpacking qiime-default-reference>=0.1.2,<0.2.0 (from qiime)
Downloading qiime-default-reference-0.1.3.tar.gz (35.2MB): 35.2MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/qiime-default-reference/setup.py) egg_info for package qiime-default-reference
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
Requirement already satisfied (use --upgrade to upgrade): six>=1.4 in /usr/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Requirement already satisfied (use --upgrade to upgrade): python-dateutil in /usr/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Requirement already satisfied (use --upgrade to upgrade): pytz in /usr/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Requirement already satisfied (use --upgrade to upgrade): pyparsing>=1.5.6 in /usr/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Requirement already satisfied (use --upgrade to upgrade): nose>=0.11.1 in /usr/local/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Downloading/unpacking mock (from matplotlib>=1.1.0,!=1.4.2->qiime)
Downloading mock-1.3.0-py2.py3-none-any.whl (56kB): 56kB downloaded
Requirement already satisfied (use --upgrade to upgrade): pyqi==0.3.2 in /usr/local/lib/python2.7/dist-packages (from biom-format>=2.1.4,<2.2.0->qiime)
Requirement already satisfied (use --upgrade to upgrade): future in /usr/local/lib/python2.7/dist-packages (from scikit-bio>=0.2.3,<0.3.0->qiime)
Requirement already satisfied (use --upgrade to upgrade): IPython in /usr/lib/python2.7/dist-packages (from scikit-bio>=0.2.3,<0.3.0->qiime)
Downloading/unpacking funcsigs (from mock->matplotlib>=1.1.0,!=1.4.2->qiime)
Downloading funcsigs-0.4-py2.py3-none-any.whl
Downloading/unpacking pbr>=0.11 (from mock->matplotlib>=1.1.0,!=1.4.2->qiime)
Downloading pbr-1.3.0-py2.py3-none-any.whl (83kB): 83kB downloaded
Installing collected packages: scipy, cogent, natsort, matplotlib, pynast, qcli, gdata, biom-format, burrito-fillings, pandas, burrito, qiime-default-reference, mock, funcsigs, pbr
Running setup.py install for scipy
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_3_10_threads_info
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_3_10_info
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
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
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_threads_info
NOT AVAILABLE
atlas_info:
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
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_info
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1505: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1516: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1519: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
NOT AVAILABLE
Running from scipy source directory.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 253, in <module>
setup_package()
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 250, in setup_package
setup(**metadata)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 175, in configuration
config.add_subpackage('scipy')
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/linalg/setup.py", line 19, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_bioinfo/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-1Tz_tu-record/install-record.txt --single-version-externally-managed --compile:
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_3_10_threads_info
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_3_10_info
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
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
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_threads_info
NOT AVAILABLE
atlas_info:
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
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_info
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1505: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1516: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1519: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
NOT AVAILABLE
Running from scipy source directory.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 253, in <module>
setup_package()
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 250, in setup_package
setup(**metadata)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 175, in configuration
config.add_subpackage('scipy')
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/linalg/setup.py", line 19, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
----------------------------------------
Cleaning up...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_bioinfo/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-1Tz_tu-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_bioinfo/scipy
Storing debug log for failure in /tmp/tmpdPltzp
Thanks,
Galen
I am trying out the QIIME tutorial on a Linux Mint distro and I have run into an error I would like advice in troubleshooting.
sudo apt-get install numpy
pip install qiime
Requirement already satisfied (use --upgrade to upgrade): qiime in /usr/local/lib/python2.7/dist-packages
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.9.0 in /usr/local/lib/python2.7/dist-packages (from qiime)
Downloading/unpacking scipy>=0.14.0 (from qiime)
Downloading scipy-0.16.0.tar.gz (18.1MB): 18.1MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/scipy/setup.py) egg_info for package scipy
warning: no previously-included files matching '*_subr_*.f' found under directory 'scipy/linalg/src/id_dist/src'
no previously-included directories found matching 'benchmarks/env'
no previously-included directories found matching 'benchmarks/results'
no previously-included directories found matching 'benchmarks/html'
no previously-included directories found matching 'benchmarks/scipy'
no previously-included directories found matching 'scipy/special/tests/data/boost'
no previously-included directories found matching 'scipy/special/tests/data/gsl'
no previously-included directories found matching 'doc/build'
no previously-included directories found matching 'doc/source/generated'
no previously-included directories found matching '*/__pycache__'
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '*.bak' found anywhere in distribution
warning: no previously-included files matching '*.swp' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
Downloading/unpacking cogent==1.5.3 (from qiime)
Downloading cogent-1.5.3.tgz (3.4MB): 3.4MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/cogent/setup.py) egg_info for package cogent
Downloading/unpacking natsort<4.0.0 (from qiime)
Downloading natsort-3.5.6-py2.py3-none-any.whl
Downloading/unpacking matplotlib>=1.1.0,!=1.4.2 (from qiime)
Downloading matplotlib-1.4.3.tar.gz (50.4MB): 50.4MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/matplotlib/setup.py) egg_info for package matplotlib
============================================================================
Edit setup.cfg to change the build options
BUILDING MATPLOTLIB
matplotlib: yes [1.4.3]
python: yes [2.7.6 (default, Jun 22 2015, 17:58:13) [GCC
4.8.2]]
platform: yes [linux2]
REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.9.2]
six: yes [using six version 1.5.2]
dateutil: yes [using dateutil version 1.5]
pytz: yes [using pytz version 2012c]
tornado: yes [using tornado version 3.1.1]
pyparsing: yes [using pyparsing version 2.0.1]
pycxx: yes [Couldn't import. Using local copy.]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
freetype: yes [version 2.5.2]
png: yes [version 1.2.50]
qhull: yes [pkg-config information for 'qhull' could not be
found. Using local copy.]
OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
tests: yes [using nose version 1.3.7 / mock is required to
run the matplotlib test suite. pip/easy_install may
attempt to install it after matplotlib.]
toolkits_tests: yes [using nose version 1.3.7 / mock is required to
run the matplotlib test suite. pip/easy_install may
attempt to install it after matplotlib.]
OPTIONAL BACKEND EXTENSIONS
macosx: no [Mac OS-X only]
qt5agg: no [PyQt5 not found]
qt4agg: yes [installing, Qt: 4.8.6, PyQt: 4.8.6]
pyside: no [PySide not found]
** (-c:16889): WARNING **: Error retrieving accessibility bus address: org.freedesktop.DBus.Error.ServiceUnknown: The name org.a11y.Bus was not provided by any .service files
gtk3agg: yes [installing, version 3.8.10]
** (-c:16900): WARNING **: Error retrieving accessibility bus address: org.freedesktop.DBus.Error.ServiceUnknown: The name org.a11y.Bus was not provided by any .service files
gtk3cairo: yes [installing, version 3.8.10]
gtkagg: no [The C/C++ header for gtk (gtk/gtk.h) could not
be found. You may need to install the development
package.]
tkagg: no [The C/C++ header for Tk (tk.h) could not be
found. You may need to install the development
package.]
wxagg: no [requires wxPython]
gtk: no [The C/C++ header for gtk (gtk/gtk.h) could not
be found. You may need to install the development
package.]
agg: yes [installing]
cairo: yes [installing, pycairo version 1.8.8]
windowing: no [Microsoft Windows only]
OPTIONAL LATEX DEPENDENCIES
dvipng: no
ghostscript: yes [version 9.10]
latex: yes [version 3.1415926]
pdftops: yes [version 0.24.5]
Downloading/unpacking pynast==1.2.2 (from qiime)
Downloading pynast-1.2.2.tar.gz (57kB): 57kB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/pynast/setup.py) egg_info for package pynast
Downloading/unpacking qcli>=0.1.1,<0.2.0 (from qiime)
Downloading qcli-0.1.1.tar.gz
Running setup.py (path:/tmp/pip_build_bioinfo/qcli/setup.py) egg_info for package qcli
Downloading/unpacking gdata (from qiime)
Downloading gdata-2.0.18.tar.gz (2.5MB): 2.5MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/gdata/setup.py) egg_info for package gdata
Downloading/unpacking biom-format>=2.1.4,<2.2.0 (from qiime)
Downloading biom-format-2.1.4.tar.gz (435kB): 435kB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/biom-format/setup.py) egg_info for package biom-format
no previously-included directories found matching 'docs/_build'
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
warning: no previously-included files matching '.git' found anywhere in distribution
Requirement already satisfied (use --upgrade to upgrade): emperor>=0.9.51,<1.0.0 in /usr/local/lib/python2.7/dist-packages (from qiime)
Requirement already satisfied (use --upgrade to upgrade): scikit-bio>=0.2.3,<0.3.0 in /usr/local/lib/python2.7/dist-packages (from qiime)
Downloading/unpacking burrito-fillings>=0.1.1,<0.2.0 (from qiime)
Downloading burrito-fillings-0.1.1.tar.gz (214kB): 214kB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/burrito-fillings/setup.py) egg_info for package burrito-fillings
Downloading/unpacking pandas>=0.13.1 (from qiime)
Downloading pandas-0.16.2.tar.gz (4.9MB): 4.9MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/pandas/setup.py) egg_info for package pandas
warning: no files found matching 'README.rst'
no previously-included directories found matching 'doc/build'
warning: no directories found matching 'examples'
warning: no previously-included files matching '*.so' found anywhere in distribution
warning: no previously-included files matching '*.pyd' found anywhere in distribution
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*~' found anywhere in distribution
warning: no previously-included files matching '#*' found anywhere in distribution
warning: no previously-included files matching '.git*' found anywhere in distribution
warning: no previously-included files matching '.DS_Store' found anywhere in distribution
warning: no previously-included files matching '*.png' found anywhere in distribution
Downloading/unpacking burrito>=0.9.1,<1.0.0 (from qiime)
Downloading burrito-0.9.1.tar.gz
Running setup.py (path:/tmp/pip_build_bioinfo/burrito/setup.py) egg_info for package burrito
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
Downloading/unpacking qiime-default-reference>=0.1.2,<0.2.0 (from qiime)
Downloading qiime-default-reference-0.1.3.tar.gz (35.2MB): 35.2MB downloaded
Running setup.py (path:/tmp/pip_build_bioinfo/qiime-default-reference/setup.py) egg_info for package qiime-default-reference
warning: no previously-included files matching '*.pyc' found anywhere in distribution
warning: no previously-included files matching '*.pyo' found anywhere in distribution
Requirement already satisfied (use --upgrade to upgrade): six>=1.4 in /usr/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Requirement already satisfied (use --upgrade to upgrade): python-dateutil in /usr/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Requirement already satisfied (use --upgrade to upgrade): pytz in /usr/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Requirement already satisfied (use --upgrade to upgrade): pyparsing>=1.5.6 in /usr/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Requirement already satisfied (use --upgrade to upgrade): nose>=0.11.1 in /usr/local/lib/python2.7/dist-packages (from matplotlib>=1.1.0,!=1.4.2->qiime)
Downloading/unpacking mock (from matplotlib>=1.1.0,!=1.4.2->qiime)
Downloading mock-1.3.0-py2.py3-none-any.whl (56kB): 56kB downloaded
Requirement already satisfied (use --upgrade to upgrade): pyqi==0.3.2 in /usr/local/lib/python2.7/dist-packages (from biom-format>=2.1.4,<2.2.0->qiime)
Requirement already satisfied (use --upgrade to upgrade): future in /usr/local/lib/python2.7/dist-packages (from scikit-bio>=0.2.3,<0.3.0->qiime)
Requirement already satisfied (use --upgrade to upgrade): IPython in /usr/lib/python2.7/dist-packages (from scikit-bio>=0.2.3,<0.3.0->qiime)
Downloading/unpacking funcsigs (from mock->matplotlib>=1.1.0,!=1.4.2->qiime)
Downloading funcsigs-0.4-py2.py3-none-any.whl
Downloading/unpacking pbr>=0.11 (from mock->matplotlib>=1.1.0,!=1.4.2->qiime)
Downloading pbr-1.3.0-py2.py3-none-any.whl (83kB): 83kB downloaded
Installing collected packages: scipy, cogent, natsort, matplotlib, pynast, qcli, gdata, biom-format, burrito-fillings, pandas, burrito, qiime-default-reference, mock, funcsigs, pbr
Running setup.py install for scipy
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_3_10_threads_info
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_3_10_info
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
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
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_threads_info
NOT AVAILABLE
atlas_info:
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
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_info
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1505: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1516: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1519: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
NOT AVAILABLE
Running from scipy source directory.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 253, in <module>
setup_package()
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 250, in setup_package
setup(**metadata)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 175, in configuration
config.add_subpackage('scipy')
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/linalg/setup.py", line 19, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
Complete output from command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_bioinfo/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-1Tz_tu-record/install-record.txt --single-version-externally-managed --compile:
lapack_opt_info:
openblas_lapack_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_3_10_threads_info
NOT AVAILABLE
atlas_3_10_info:
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_3_10_info
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
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
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_threads_info
NOT AVAILABLE
atlas_info:
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
libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
numpy.distutils.system_info.atlas_info
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1505: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.__doc__)
lapack_info:
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1516: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
warnings.warn(LapackNotFoundError.__doc__)
lapack_src_info:
NOT AVAILABLE
/usr/local/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1519: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
warnings.warn(LapackSrcNotFoundError.__doc__)
NOT AVAILABLE
Running from scipy source directory.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 253, in <module>
setup_package()
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 250, in setup_package
setup(**metadata)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "/tmp/pip_build_bioinfo/scipy/setup.py", line 175, in configuration
config.add_subpackage('scipy')
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/usr/local/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/linalg/setup.py", line 19, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found
----------------------------------------
Cleaning up...
Command /usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_bioinfo/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-1Tz_tu-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_bioinfo/scipy
Storing debug log for failure in /tmp/tmpdPltzp
Thanks,
Galen
Tony Walters
Jul 28, 2015, 8:03:29 PM7/28/15
to qiime...@googlegroups.com
Hello Galen,
Someone ran into a similar problem in this thread: https://groups.google.com/forum/#!searchin/qiime-forum/%5Bqiime-forum$201.9.0%5D$20Native$20install$20on$20Ubuntu$2014.04$20LTS/qiime-forum/8dVlTtlg59M/X3aUWH6DOQMJ
Can you try the approach used in that thread and see if it fixes the dependency issue?
Can you try the approach used in that thread and see if it fixes the dependency issue?
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