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Custom Heroku buildpack for Python with NumPy and SciPy
License: MIT License
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Time out compiling
Hi! First off, thanks so much for the awesome buildpack!
I've used it in the past, but recently, whenever I've tried to push to Heroku with this buildpack, it times out while compiling Numpy.
Timed out compiling Python app (15 minutes)
Any hints or tips? I've seen people create a custom buildpack to download precompiled binaries, but I would love to avoid that if possible. Have you seen this before?
Thanks!
Dylan
netcdf/hdf5 support?
I'm trying to get a numpy/scipy project running on heroku, but the project requires the use of netcdf and hdf5. I'm new to buildpacks generally, but this one seems like a great place to start. Any suggestions as to how to proceed? I have compiled netcdf and hdf5 binaries on heroku, but integrating them into the buildpack and getting pip to 'do the right thing' has proven difficult.
undefined symbol: cblas_dasum
After deployment the import error raised during runtime. The error report as follow:
ImportError: /app/.heroku/python/lib/python2.7/site-packages/sklearn/metrics/pairwise_fast.so: undefined symbol: cblas_dasum
Error installing scikit-learn on top of scipy+numpy
For a requirements.txt file just like
numpy==1.8.1
scipy==0.14.0
scikit-learn==0.14.1
Current version gives me
ImportError: liblapack.so.3gf:
I had to rollback to commit 1a9ab58 to make it work. I believe the change from export to set-env might be behind the error (so libraries dont get added to LDPATH)
build scripts for binaries
Could you please provide the building and packaging scripts for NumPy, SciPy, and the dependencies? I checked here, but was unable to find them.
It would be great to verify how they are be compiled and with what compile time options.
Thanks!
Support Python 3.4.1 runtime?
Thanks for this very useful buildpack! Is there any way to get it working with 3.4?
Error while import hierarchy
Hi,
On the heroku app, I compiled Scipy 0.13.3 with Numpy 1.9 using the toolbelt. Now I am getting following error when import hiegharchy. Here's the the tracestack:
from . import vq, hierarchy
File "/app/.heroku/python/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 175, in <module>
from . import _hierarchy_wrap
ImportError: cannot import name _hierarchy_wrap
Unpickler(file).load() issue undefined symbol: cblas_drot
Flask
Atlas
numpy==1.9.2
scipy==0.15.1
scikit-learn==0.17
ERR Traceback (most recent call last):
2015-11-08T18:56:33.42-0800 [App/0] ERR File "hello.py", line 244, in
2015-11-08T18:56:33.42-0800 [App/0] ERR clf_hydrated = pickle.loads(svm_rbf_triple)
2015-11-08T18:56:33.42-0800 [App/0] ERR File "/app/.heroku/python/lib/python2.7/pickle.py", line 1382, in loads
2015-11-08T18:56:33.42-0800 [App/0] ERR return Unpickler(file).load()
2015-11-08T18:56:33.42-0800 [App/0] ERR File "/app/.heroku/python/lib/python2.7/pickle.py", line 858, in load
2015-11-08T18:56:33.42-0800 [App/0] ERR dispatchkey
2015-11-08T18:56:33.42-0800 [App/0] ERR File "/app/.heroku/python/lib/python2.7/pickle.py", line 1090, in load_global
2015-11-08T18:56:33.42-0800 [App/0] ERR klass = self.find_class(module, name)
2015-11-08T18:56:33.42-0800 [App/0] ERR File "/app/.heroku/python/lib/python2.7/pickle.py", line 1124, in find_class
2015-11-08T18:56:33.42-0800 [App/0] ERR import(module)
2015-11-08T18:56:33.42-0800 [App/0] ERR File "/app/.heroku/python/lib/python2.7/site-packages/sklearn/linear_model/init.py", line 15, in
2015-11-08T18:56:33.42-0800 [App/0] ERR from .least_angle import (Lars, LassoLars, lars_path, LarsCV, LassoLarsCV,
2015-11-08T18:56:33.42-0800 [App/0] ERR File "/app/.heroku/python/lib/python2.7/site-packages/sklearn/linear_model/least_angle.py", line 24, in
2015-11-08T18:56:33.42-0800 [App/0] ERR from ..utils import arrayfuncs, as_float_array, check_X_y
2015-11-08T18:56:33.42-0800 [App/0] ERR ImportError: /app/.heroku/python/lib/python2.7/site-packages/sklearn/utils/arrayfuncs.so: undefined symbol: cblas_drot
2015-11-08T18:56:33.44-0800 [App/0] OUT
2015-11-08T18:56:33.46-0800 [DEA/26] ERR Instance (index 0) failed to start accepting connections
undefined symbol: cblas_drot
I believe we are hitting some dependency issues after upgrading to the newest scipy/numpy
Here is the installation of the newest packages: https://gist.github.com/beedub/43d10721887ab5668a0b
Then we get a runtime error for sklearn/utils/arrayfuncs.so: undefined symbol: cblas_drot: https://gist.github.com/beedub/bacf2f52e2a3fe1544e7
So I'm guessing this is a problem with the buildpacks installation of BLAS?
ImportError: No module named 'pip._vendor.requests'
Hi, I've been using your buildpack for a last month and it's been working fine but when I want to create new application it fails on this:
2016-03-21T17:30:07.31+0100 [STG/210] OUT -----> Downloaded app package (20K)
2016-03-21T17:30:07.46+0100 [STG/0] ERR Cloning into '/tmp/buildpacks/heroku-buildpack-scipy'...
2016-03-21T17:30:26.36+0100 [STG/0] OUT -----> Installing runtime (python-2.7.10)
2016-03-21T17:30:42.41+0100 [STG/0] OUT -----> Installing dependencies with pip
2016-03-21T17:30:42.63+0100 [STG/0] ERR ERROR:root:code for hash md5 was not found.
2016-03-21T17:30:42.63+0100 [STG/0] ERR Traceback (most recent call last):
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 147, in <module>
2016-03-21T17:30:42.63+0100 [STG/0] ERR globals()[__func_name] = __get_hash(__func_name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
2016-03-21T17:30:42.63+0100 [STG/0] ERR raise ValueError('unsupported hash type ' + name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR ValueError: unsupported hash type md5
2016-03-21T17:30:42.63+0100 [STG/0] ERR ERROR:root:code for hash sha1 was not found.
2016-03-21T17:30:42.63+0100 [STG/0] ERR Traceback (most recent call last):
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 147, in <module>
2016-03-21T17:30:42.63+0100 [STG/0] ERR globals()[__func_name] = __get_hash(__func_name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
2016-03-21T17:30:42.63+0100 [STG/0] ERR raise ValueError('unsupported hash type ' + name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR ValueError: unsupported hash type sha1
2016-03-21T17:30:42.63+0100 [STG/0] ERR ERROR:root:code for hash sha224 was not found.
2016-03-21T17:30:42.63+0100 [STG/0] ERR Traceback (most recent call last):
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 147, in <module>
2016-03-21T17:30:42.63+0100 [STG/0] ERR globals()[__func_name] = __get_hash(__func_name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
2016-03-21T17:30:42.63+0100 [STG/0] ERR raise ValueError('unsupported hash type ' + name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR ValueError: unsupported hash type sha224
2016-03-21T17:30:42.63+0100 [STG/0] ERR ERROR:root:code for hash sha256 was not found.
2016-03-21T17:30:42.63+0100 [STG/0] ERR Traceback (most recent call last):
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 147, in <module>
2016-03-21T17:30:42.63+0100 [STG/0] ERR globals()[__func_name] = __get_hash(__func_name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
2016-03-21T17:30:42.63+0100 [STG/0] ERR raise ValueError('unsupported hash type ' + name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR ValueError: unsupported hash type sha256
2016-03-21T17:30:42.63+0100 [STG/0] ERR ERROR:root:code for hash sha384 was not found.
2016-03-21T17:30:42.63+0100 [STG/0] ERR Traceback (most recent call last):
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 147, in <module>
2016-03-21T17:30:42.63+0100 [STG/0] ERR globals()[__func_name] = __get_hash(__func_name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
2016-03-21T17:30:42.63+0100 [STG/0] ERR raise ValueError('unsupported hash type ' + name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR ValueError: unsupported hash type sha384
2016-03-21T17:30:42.63+0100 [STG/0] ERR ERROR:root:code for hash sha512 was not found.
2016-03-21T17:30:42.63+0100 [STG/0] ERR Traceback (most recent call last):
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 147, in <module>
2016-03-21T17:30:42.63+0100 [STG/0] ERR globals()[__func_name] = __get_hash(__func_name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/hashlib.py", line 97, in __get_builtin_constructor
2016-03-21T17:30:42.63+0100 [STG/0] ERR raise ValueError('unsupported hash type ' + name)
2016-03-21T17:30:42.63+0100 [STG/0] ERR ValueError: unsupported hash type sha512
2016-03-21T17:30:42.77+0100 [STG/0] ERR Traceback (most recent call last):
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "/app/.heroku/python/bin/pip", line 9, in <module>
2016-03-21T17:30:42.77+0100 [STG/0] ERR load_entry_point('pip==6.0.6', 'console_scripts', 'pip')()
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 519, in load_entry_point
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2630, in load_entry_point
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2310, in load
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", line 2316, in resolve
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/__init__.py", line 15, in <module>
2016-03-21T17:30:42.77+0100 [STG/0] ERR from pip.vcs import git, mercurial, subversion, bazaar # noqa
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/vcs/mercurial.py", line 11, in <module>
2016-03-21T17:30:42.77+0100 [STG/0] ERR from pip.download import path_to_url
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/download.py", line 30, in <module>
2016-03-21T17:30:42.77+0100 [STG/0] ERR from pip._vendor import requests, six
2016-03-21T17:30:42.77+0100 [STG/0] ERR File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/_vendor/__init__.py", line 81, in load_module
2016-03-21T17:30:42.77+0100 [STG/0] ERR raise ImportError("No module named '%s'" % (name,))
2016-03-21T17:30:42.77+0100 [STG/0] ERR ImportError: No module named 'pip._vendor.requests'
2016-03-21T17:30:42.80+0100 [STG/0] OUT Staging failed: Buildpack compilation step failed
2016-03-21T17:30:42.99+0100 [API/0] ERR encountered error: App staging failed in the buildpack compile phase
The content of requirements.txt doesn't matter, if i have that file empty the build still fails. I think that it has something to do with new stack cf_linuxfs2 based on this issue https://developer.ibm.com/answers/questions/236264/bluemix-and-python-deploy-error-after-platform-upg.html but I dont really know what that means or how to fix it. My knowledge of buildpacks is basically none.
One last thing - if i try to print state of my app the log says
$ cf app my_app
Showing health and status for app my_app in org ... / space ... as ...
FAILED
Server error, status code: 400, error code: 170004, message: App staging failed in the buildpack compile phase
Heroku logs disappearing
Any apps I create which use this buildpack compile fine, but running the "heroku logs" command no longer shows any errors, making debugging impossible. The logs don't show any of my "console.error()" or "console.log()" messages which should be appearing.
Fortran compiler found
I have been trying to use this tool and it seems awesome! Thanks for making it! 👍 But at the very end of running:
git push heroku master
and installing everything I get this:
building 'dfftpack' library
error: library dfftpack has Fortran sources but no Fortran compiler found
Any thoughts on why that would be missing?
error: library dfftpack has Fortran sources but no Fortran compiler found
I encounter an error when building 'dfftpack' library on heroku. It seems that there is no fortran compiler in heroku so dfftpack library cannot be built. How can I solve this problem?
Update to numpy 1.9.0
Any plan to update this to numpy 1.9.0?
Issues with python3 runtime
I had some issues using this buildpack with my code running the python 3.4.1 runtime, so I tried to find a minimal example. It turns out that if you follow the demo steps provided in the README, but add a runtime.txt file that specifies python-3.4.1, the initial push fails. It looks like pip doesn't see the pre-installed binary packages and tries to rebuild numpy from source (which will of course fail).
Here's some sample output: https://gist.github.com/HapeMask/ba6d8d924ba002f2c9ad
Normally, when following the demo on a python 2.X runtime, it would just say "Cleaning up" on line 21 of the above gist, but instead it's building everything again. I didn't get a chance to dig deeper yet (going to sleep) but I'll look into it more tomorrow.
scipy 0.15.1
We're trying to build an app with the most recent version of SciPy. Are there plans to update this in the near future?
BTW, we were able to deploy the current buildpack on the new cedar-14 stack without issue.
ImportError: Numerical Python (NumPy) is not installed.
Hello, I a trying to use the buildpack in my heroku project.
My requirements.txt has
numpy==1.8.1
scipy==0.14.0
scikit-learn==0.17b1
I am using python-2.7.10
I've done
heroku buildpacks:set https://github.com/thenovices/heroku-buildpack-scipy
I get
ImportError: Numerical Python (NumPy) is not installed.
I got some error in the process like
-----> Downloading BLAS/LAPACK/ATLAS/Fortran binaries.
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
Traceback (most recent call last):
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 81, in <module>
main()
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 77, in main
grep(**kwargs)
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 45, in grep
r = Requirements(reqfile)
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 27, in __init__
self.load(reqfile)
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 38, in load
for requirement in parse_requirements(reqfile, finder=finder, session=requests):
File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/req/req_file.py", line 129, in parse_requirements
isolated=options.isolated_mode if options else False,
File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/req/req_install.py", line 92, in from_editable
editable_req, default_vcs)
File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/req/req_install.py", line 1045, in parse_editable
url_no_extras
pip.exceptions.InstallationError: Directory '.' is not installable. File 'setup.py' not found.
Traceback (most recent call last):
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 81, in <module>
main()
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 77, in main
grep(**kwargs)
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 45, in grep
r = Requirements(reqfile)
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 27, in __init__
self.load(reqfile)
File "/tmp/buildpack20151106-157-n5ixfp/vendor/pip-pop/pip-grep", line 38, in load
for requirement in parse_requirements(reqfile, finder=finder, session=requests):
File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/req/req_file.py", line 129, in parse_requirements
isolated=options.isolated_mode if options else False,
File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/req/req_install.py", line 92, in from_editable
editable_req, default_vcs)
File "/app/.heroku/python/lib/python2.7/site-packages/pip-6.0.6-py2.7.egg/pip/req/req_install.py", line 1045, in parse_editable
url_no_extras
pip.exceptions.InstallationError: Directory '.' is not installable. File 'setup.py' not found.
remote: /tmp/easy_install-g1b60o/numpy-1.10.1/_configtest.c:6: undefined reference to `exp'
remote: collect2: error: ld returned 1 exit status
remote: _configtest.o: In function `main':
remote: /tmp/easy_install-g1b60o/numpy-1.10.1/_configtest.c:6: undefined reference to `exp'
remote: collect2: error: ld returned 1 exit status
Any idea what I could do? Thanks
Is there any environment variable needed, apart from the BUILDPACK one?
My requirements include the following (in that order):
Cython==0.20.2 # Compiles fine.
numpy==1.8.1
# ...
scipy==0.14.0
However, on deploy, I get the following error (after Cython compiles correctly, and numpy starts to compile correctly). Any thoughts on the reasons why this can happen?
gcc: numpy/random/mtrand/randomkit.c
gcc -pthread -shared build/temp.linux-x86_64-2.7/numpy/random/mtrand/mtrand.o build/temp.linux-x86_64-2.7/numpy/random/mtrand/randomkit.o build/temp.linux-x86_64-2.7/numpy/random/mtrand/initarray.o build/temp.linux-x86_64-2.7/numpy/random/mtrand/distributions.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7/numpy/random/mtrand.so
Creating build/scripts.linux-x86_64-2.7/f2py
adding 'build/scripts.linux-x86_64-2.7/f2py' to scripts
changing mode of build/scripts.linux-x86_64-2.7/f2py from 600 to 755
warning: no files found matching 'tools/py3tool.py'
warning: no files found matching '*' under directory 'doc/f2py'
changing mode of /app/.heroku/python/bin/f2py to 755
Running setup.py install for scipy
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
openblas_info:
libraries not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: 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:
libraries blas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1530: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
NOT AVAILABLE
/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1533: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
warnings.warn(BlasSrcNotFoundError.__doc__)
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-u6095/scipy/setup.py", line 237, in <module>
setup_package()
File "/tmp/pip-build-u6095/scipy/setup.py", line 234, in setup_package
setup(**metadata)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "/tmp/pip-build-u6095/scipy/setup.py", line 173, in configuration
config.add_subpackage('scipy')
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/setup.py", line 12, in configuration
config.add_subpackage('integrate')
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/integrate/setup.py", line 12, in configuration
blas_opt = get_info('blas_opt',notfound_action=2)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info
return cl().get_info(notfound_action)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info
raise self.notfounderror(self.notfounderror.__doc__)
numpy.distutils.system_info.BlasNotFoundError:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
Complete output from command /app/.heroku/python/bin/python -c "import setuptools;__file__='/tmp/pip-build-u6095/scipy/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-t2O5oi-record/install-record.txt --single-version-externally-managed:
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
openblas_info:
libraries not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: 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:
libraries blas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE
/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1530: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
warnings.warn(BlasNotFoundError.__doc__)
blas_src_info:
NOT AVAILABLE
/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1533: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
warnings.warn(BlasSrcNotFoundError.__doc__)
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-u6095/scipy/setup.py", line 237, in <module>
setup_package()
File "/tmp/pip-build-u6095/scipy/setup.py", line 234, in setup_package
setup(**metadata)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
config = configuration()
File "/tmp/pip-build-u6095/scipy/setup.py", line 173, in configuration
config.add_subpackage('scipy')
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/setup.py", line 12, in configuration
config.add_subpackage('integrate')
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
caller_level = 2)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
caller_level = caller_level + 1)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/integrate/setup.py", line 12, in configuration
blas_opt = get_info('blas_opt',notfound_action=2)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info
return cl().get_info(notfound_action)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info
raise self.notfounderror(self.notfounderror.__doc__)
numpy.distutils.system_info.BlasNotFoundError:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
----------------------------------------
Command /app/.heroku/python/bin/python -c "import setuptools;__file__='/tmp/pip-build-u6095/scipy/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-t2O5oi-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip-build-u6095/scipy
Storing complete log in /app/.pip/pip.log
! Push rejected, failed to compile Python app
Any plans to update to scikit-learn 1.5.0?
This project is great! Are there any plans to upgrade to the new scikit-learn?
Numpy 1.9.2 test failures
Here were my test results on numpy 1.9.2: one test failure; not really sure what to do about it.
Running unit tests for numpy
NumPy version 1.9.2
NumPy is installed in /app/.heroku/python/lib/python2.7/site-packages/numpy
Python version 2.7.8 (default, Jul 9 2014, 20:47:08) [GCC 4.4.3]
nose version 1.3.3
............................S.........S..............................................................................................................................................................................................................................................................................................................................................SS...........................................................................................S....................................................................................................................S................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K.........................................................................SSSSS.........................................K......................K.............................................................................................................ESS....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................K...........................................................
======================================================================
ERROR: Failure: ValueError (Empty module name)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/app/.heroku/python/lib/python2.7/site-packages/nose/loader.py", line 414, in loadTestsFromName
addr.filename, addr.module)
File "/app/.heroku/python/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
return self.importFromDir(dir_path, fqname)
File "/app/.heroku/python/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
mod = load_module(part_fqname, fh, filename, desc)
File "/app/.heroku/python/lib/python2.7/site-packages/numpy/doc/__init__.py", line 11, in <module>
__import__(__name__ + '.' + f)
ValueError: Empty module name
----------------------------------------------------------------------
Ran 5236 tests in 45.756s
Cannot compile on classic cedar stack
installing with
numpy==1.8.1
scipy==0.14.0
remote: building 'numpy.random.mtrand' extension
remote: compiling C sources
remote: C compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
remote:
remote: compile options: '-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -Inumpy/core/include -Ibuild/src.linux-
rc/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -In
thon2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/nump
mpy/core/src/private -c'
remote: gcc: numpy/random/mtrand/distributions.c
remote: gcc: numpy/random/mtrand/mtrand.c
remote: gcc: numpy/random/mtrand/initarray.c
remote: build/src.linux-x86_64-2.7/numpy/core/include/numpy/__multiarray_api.h:1629: warning: ‘_import_array’ defined but not used
remote: gcc: numpy/random/mtrand/randomkit.c
remote: gcc -pthread -shared build/temp.linux-x86_64-2.7/numpy/random/mtrand/mtrand.o build/temp.linux-x86_64-2.7/numpy/random/mtrand/
om/mtrand/initarray.o build/temp.linux-x86_64-2.7/numpy/random/mtrand/distributions.o -Lbuild/temp.linux-x86_64-2.7 -o build/lib.linux-x86_64-2.7
remote: Creating build/scripts.linux-x86_64-2.7/f2py
remote: adding 'build/scripts.linux-x86_64-2.7/f2py' to scripts
remote: changing mode of build/scripts.linux-x86_64-2.7/f2py from 600 to 755
remote:
remote: warning: no files found matching 'tools/py3tool.py'
remote: warning: no files found matching '*' under directory 'doc/f2py'
remote: changing mode of /app/.heroku/python/bin/f2py to 755
remote: Running setup.py install for scipy
remote: blas_opt_info:
remote: blas_mkl_info:
remote: libraries mkl,vml,guide not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote: NOT AVAILABLE
remote:
remote: openblas_info:
remote: libraries not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote: NOT AVAILABLE
remote:
remote: atlas_blas_threads_info:
remote: Setting PTATLAS=ATLAS
remote: libraries ptf77blas,ptcblas,atlas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote: NOT AVAILABLE
remote:
remote: atlas_blas_info:
remote: libraries f77blas,cblas,atlas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote: NOT AVAILABLE
remote:
remote: /app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: UserWarning:
remote: Atlas (http://math-atlas.sourceforge.net/) libraries not found.
remote: Directories to search for the libraries can be specified in the
remote: numpy/distutils/site.cfg file (section [atlas]) or by setting
remote: the ATLAS environment variable.
remote: warnings.warn(AtlasNotFoundError.__doc__)
remote: blas_info:
remote: libraries blas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote: NOT AVAILABLE
remote:
remote: /app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1530: UserWarning:
remote: Blas (http://www.netlib.org/blas/) libraries not found.
remote: Directories to search for the libraries can be specified in the
remote: numpy/distutils/site.cfg file (section [blas]) or by setting
remote: the BLAS environment variable.
remote: warnings.warn(BlasNotFoundError.__doc__)
remote: blas_src_info:
remote: NOT AVAILABLE
remote:
remote: /app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1533: UserWarning:
remote: Blas (http://www.netlib.org/blas/) sources not found.
remote: Directories to search for the sources can be specified in the
remote: numpy/distutils/site.cfg file (section [blas_src]) or by setting
remote: the BLAS_SRC environment variable.
remote: warnings.warn(BlasSrcNotFoundError.__doc__)
remote: Traceback (most recent call last):
remote: File "", line 1, in
remote: File "/tmp/pip_build_u8769/scipy/setup.py", line 237, in
remote: setup_package()
remote: File "/tmp/pip_build_u8769/scipy/setup.py", line 234, in setup_package
remote: setup(**metadata)
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
remote: config = configuration()
remote: File "/tmp/pip_build_u8769/scipy/setup.py", line 173, in configuration
remote: config.add_subpackage('scipy')
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
remote: caller_level = 2)
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
remote: caller_level = caller_level + 1)
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_se
remote: config = setup_module.configuration(*args)
remote: File "scipy/setup.py", line 12, in configuration
remote: config.add_subpackage('integrate')
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
remote: caller_level = 2)
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
remote: caller_level = caller_level + 1)
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_se
remote: config = setup_module.configuration(*args)
remote: File "scipy/integrate/setup.py", line 12, in configuration
remote: blas_opt = get_info('blas_opt',notfound_action=2)
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info
remote: return cl().get_info(notfound_action)
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info
remote: raise self.notfounderror(self.notfounderror.__doc__)
remote: numpy.distutils.system_info.BlasNotFoundError:
remote: Blas (http://www.netlib.org/blas/) libraries not found.
remote: Directories to search for the libraries can be specified in the
remote: numpy/distutils/site.cfg file (section [blas]) or by setting
remote: the BLAS environment variable.
remote: Complete output from command /app/.heroku/python/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_u8769/sci
, open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-0GYDl_-record/install-record.txt --single-version-e
remote: blas_opt_info:
remote:
remote: blas_mkl_info:
remote:
remote: libraries mkl,vml,guide not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote:
remote: NOT AVAILABLE
remote:
remote:
remote:
remote: openblas_info:
remote:
remote: libraries not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote:
remote: NOT AVAILABLE
remote:
remote:
remote:
remote: atlas_blas_threads_info:
remote:
remote: Setting PTATLAS=ATLAS
remote:
remote: libraries ptf77blas,ptcblas,atlas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote:
remote: NOT AVAILABLE
remote:
remote:
remote:
remote: atlas_blas_info:
remote:
remote: libraries f77blas,cblas,atlas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote:
remote: NOT AVAILABLE
remote:
remote:
remote:
remote: /app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1521: UserWarning:
remote:
remote: Atlas (http://math-atlas.sourceforge.net/) libraries not found.
remote:
remote: Directories to search for the libraries can be specified in the
remote:
remote: numpy/distutils/site.cfg file (section [atlas]) or by setting
remote:
remote: the ATLAS environment variable.
remote:
remote: warnings.warn(AtlasNotFoundError.__doc__)
remote:
remote: blas_info:
remote:
remote: libraries blas not found in ['/app/.heroku/python/lib', '/usr/local/lib', '/usr/lib64', '/usr/lib']
remote:
remote: NOT AVAILABLE
remote:
remote:
remote:
remote: /app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1530: UserWarning:
remote:
remote: Blas (http://www.netlib.org/blas/) libraries not found.
remote:
remote: Directories to search for the libraries can be specified in the
remote:
remote: numpy/distutils/site.cfg file (section [blas]) or by setting
remote:
remote: the BLAS environment variable.
remote:
remote: warnings.warn(BlasNotFoundError.__doc__)
remote:
remote: blas_src_info:
remote:
remote: NOT AVAILABLE
remote:
remote:
remote:
remote: /app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py:1533: UserWarning:
remote:
remote: Blas (http://www.netlib.org/blas/) sources not found.
remote:
remote: Directories to search for the sources can be specified in the
remote:
remote: numpy/distutils/site.cfg file (section [blas_src]) or by setting
remote:
remote: the BLAS_SRC environment variable.
remote:
remote: warnings.warn(BlasSrcNotFoundError.__doc__)
remote:
remote: Traceback (most recent call last):
remote:
remote: File "", line 1, in
remote:
remote: File "/tmp/pip_build_u8769/scipy/setup.py", line 237, in
remote:
remote: setup_package()
remote:
remote: File "/tmp/pip_build_u8769/scipy/setup.py", line 234, in setup_package
remote:
remote: setup(**metadata)
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/core.py", line 135, in setup
remote:
remote: config = configuration()
remote:
remote: File "/tmp/pip_build_u8769/scipy/setup.py", line 173, in configuration
remote:
remote: config.add_subpackage('scipy')
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
remote:
remote: caller_level = 2)
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
remote:
remote: caller_level = caller_level + 1)
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_
remote:
remote: config = setup_module.configuration(*args)
remote:
remote: File "scipy/setup.py", line 12, in configuration
remote:
remote: config.add_subpackage('integrate')
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
remote:
remote: caller_level = 2)
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
remote:
remote: caller_level = caller_level + 1)
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_
remote:
remote: config = setup_module.configuration(*args)
remote:
remote: File "scipy/integrate/setup.py", line 12, in configuration
remote:
remote: blas_opt = get_info('blas_opt',notfound_action=2)
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 350, in get_info
remote:
remote: return cl().get_info(notfound_action)
remote:
remote: File "/app/.heroku/python/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 509, in get_info
remote:
remote: raise self.notfounderror(self.notfounderror.__doc__)
remote:
remote: numpy.distutils.system_info.BlasNotFoundError:
remote:
remote: Blas (http://www.netlib.org/blas/) libraries not found.
remote:
remote: Directories to search for the libraries can be specified in the
remote:
remote: numpy/distutils/site.cfg file (section [blas]) or by setting
remote:
remote: the BLAS environment variable.
remote:
remote: ----------------------------------------
remote: Cleaning up...
remote: Command /app/.heroku/python/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip_build_u8769/scipy/setup.py';exec(compile
replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-0GYDl_-record/install-record.txt --single-version-externally-managed --compi
9/scipy
remote: Traceback (most recent call last):
remote: File "/app/.heroku/python/bin/pip", line 9, in
remote: load_entry_point('pip==1.5.6', 'console_scripts', 'pip')()
remote: File "/app/.heroku/python/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/__init__.py", line 185, in main
remote: return command.main(cmd_args)
remote: File "/app/.heroku/python/lib/python2.7/site-packages/pip-1.5.6-py2.7.egg/pip/basecommand.py", line 161, in main
remote: text = '\n'.join(complete_log)
remote: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 70: ordinal not in range(128)
remote:
remote: ! Push rejected, failed to compile Multipack app
remote:
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