NeuroNER installation on Windows about neuroner HOT 10 CLOSED

I would be glad to assist you. Which step of https://github.com/Franck-Dernoncourt/NeuroNER/blob/master/install_windows.md is unclear to you?

from neuroner.

Thanks for the quick response. I have reset my windows in order to get rid of the previous installation and started the installation again. For the first step "Python 3.5, TensorFlow, and several other Python packages" i have installed them by following the instructions in the link
Just for your knowledge i have installed tensorflow by using
pip3 install --upgrade tensorflow (instead of ip install tensorflow)

but for the command

pip install -U networkx matplotlib scikit-learn scipy pycorenlp

ALL OTHER PACKAGES INSTALLED SUCCESSFULLY BUT spicy package installation failed with an error pasted below(Sorry for the long text)...........
Kindly guide me how i can resolve this error first

Building wheels for collected packages: scipy, pycorenlp
Running setup.py bdist_wheel for scipy ... error
Complete output from command c:\users\zill-e-huma\appdata\local\programs\python\python35\python.exe -u -c "import setuptools, tokenize;file='C:\Users\ZILL-E1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" bdist_wheel -d C:\Users\ZILL-E1\AppData\Local\Temp\tmpoe7xon70pip-wheel- --python-tag cp35:
lapack_opt_info:
lapack_mkl_info:
libraries mkl_rt not found in ['c:\users\zill-e-huma\appdata\local\programs\python\python35\lib', 'C:\', 'c:\users\zill-e-huma\appdata\local\programs\python\python35\libs']
NOT AVAILABLE

openblas_lapack_info:
libraries openblas not found in ['c:\users\zill-e-huma\appdata\local\programs\python\python35\lib', 'C:\', 'c:\users\zill-e-huma\appdata\local\programs\python\python35\libs']
NOT AVAILABLE

atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\system_info.py:1051: UserWarning: Specified path C:\projects\numpy-wheels-jc1cl\windows-wheel-builder\atlas-builds\atlas-3.11.38-sse2-64\lib is invalid.
pre_dirs = system_info.get_paths(self, section, key)
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE

atlas_3_10_info:
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE

atlas_info:
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE

c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
lapack_info:
libraries lapack not found in ['c:\users\zill-e-huma\appdata\local\programs\python\python35\lib', 'C:\', 'c:\users\zill-e-huma\appdata\local\programs\python\python35\libs']
NOT AVAILABLE

c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
self.calc_info()
lapack_src_info:
NOT AVAILABLE

c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
self.calc_info()
NOT AVAILABLE

Running from scipy source directory.
non-existing path in 'scipy\integrate': 'quadpack.h'
Traceback (most recent call last):
File "", line 1, in
File "C:\Users\ZILL-E1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py", line 416, in
setup_package()
File "C:\Users\ZILL-E1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py", line 412, in setup_package
setup(**metadata)
File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\core.py", line 135, in setup
config = configuration()
File "C:\Users\ZILL-E~1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py", line 336, in configuration
config.add_subpackage('scipy')
File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 1029, in add_subpackage
caller_level = 2)
File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 998, in get_subpackage
caller_level = caller_level + 1)
File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 935, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\setup.py", line 15, in configuration
config.add_subpackage('linalg')
File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 1029, in add_subpackage
caller_level = 2)
File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 998, in get_subpackage
caller_level = caller_level + 1)
File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 935, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy\linalg\setup.py", line 20, in configuration
raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

Failed building wheel for scipy
Running setup.py clean for scipy
Complete output from command c:\users\zill-e-huma\appdata\local\programs\python\python35\python.exe -u -c "import setuptools, tokenize;file='C:\Users\ZILL-E~1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" clean --all:

setup.py clean is not supported, use one of the following instead:

- `git clean -xdf` (cleans all files)
- `git clean -Xdf` (cleans all versioned files, doesn't touch
                    files that aren't checked into the git repo)

Add --force to your command to use it anyway if you must (unsupported).

Failed cleaning build dir for scipy
Running setup.py bdist_wheel for pycorenlp ... done
Stored in directory: C:\Users\Zill-E-Huma\AppData\Local\pip\Cache\wheels\7d\a4\5f\c53f3d7ec0338384640719996d72ddb6d3a9a0f6b095b634f5
Successfully built pycorenlp
Failed to build scipy
Installing collected packages: decorator, networkx, cycler, pyparsing, pytz, python-dateutil, matplotlib, scikit-learn, scipy, idna, chardet, certifi, urllib3, requests, pycorenlp
Running setup.py install for scipy ... error
Complete output from command c:\users\zill-e-huma\appdata\local\programs\python\python35\python.exe -u -c "import setuptools, tokenize;file='C:\Users\ZILL-E1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record C:\Users\ZILL-E1\AppData\Local\Temp\pip-1ofstwft-record\install-record.txt --single-version-externally-managed --compile:

Note: if you need reliable uninstall behavior, then install
with pip instead of using `setup.py install`:

  - `pip install .`       (from a git repo or downloaded source
                           release)
  - `pip install scipy`   (last SciPy release on PyPI)


lapack_opt_info:
lapack_mkl_info:
  libraries mkl_rt not found in ['c:\\users\\zill-e-huma\\appdata\\local\\programs\\python\\python35\\lib', 'C:\\', 'c:\\users\\zill-e-huma\\appdata\\local\\programs\\python\\python35\\libs']
  NOT AVAILABLE

openblas_lapack_info:
  libraries openblas not found in ['c:\\users\\zill-e-huma\\appdata\\local\\programs\\python\\python35\\lib', 'C:\\', 'c:\\users\\zill-e-huma\\appdata\\local\\programs\\python\\python35\\libs']
  NOT AVAILABLE

atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\system_info.py:1051: UserWarning: Specified path C:\projects\numpy-wheels-jc1cl\windows-wheel-builder\atlas-builds\atlas-3.11.38-sse2-64\lib is invalid.
  pre_dirs = system_info.get_paths(self, section, key)
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
  NOT AVAILABLE

atlas_3_10_info:
<class 'numpy.distutils.system_info.atlas_3_10_info'>
  NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
<class 'numpy.distutils.system_info.atlas_threads_info'>
  NOT AVAILABLE

atlas_info:
<class 'numpy.distutils.system_info.atlas_info'>
  NOT AVAILABLE

c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
    Atlas (http://math-atlas.sourceforge.net/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [atlas]) or by setting
    the ATLAS environment variable.
  self.calc_info()
lapack_info:
  libraries lapack not found in ['c:\\users\\zill-e-huma\\appdata\\local\\programs\\python\\python35\\lib', 'C:\\', 'c:\\users\\zill-e-huma\\appdata\\local\\programs\\python\\python35\\libs']
  NOT AVAILABLE

c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
    Lapack (http://www.netlib.org/lapack/) libraries not found.
    Directories to search for the libraries can be specified in the
    numpy/distutils/site.cfg file (section [lapack]) or by setting
    the LAPACK environment variable.
  self.calc_info()
lapack_src_info:
  NOT AVAILABLE

c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\system_info.py:572: UserWarning:
    Lapack (http://www.netlib.org/lapack/) sources not found.
    Directories to search for the sources can be specified in the
    numpy/distutils/site.cfg file (section [lapack_src]) or by setting
    the LAPACK_SRC environment variable.
  self.calc_info()
  NOT AVAILABLE

Running from scipy source directory.
non-existing path in 'scipy\\integrate': 'quadpack.h'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "C:\Users\ZILL-E~1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py", line 416, in <module>
    setup_package()
  File "C:\Users\ZILL-E~1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py", line 412, in setup_package
    setup(**metadata)
  File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\core.py", line 135, in setup
    config = configuration()
  File "C:\Users\ZILL-E~1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py", line 336, in configuration
    config.add_subpackage('scipy')
  File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 1029, in add_subpackage
    caller_level = 2)
  File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 998, in get_subpackage
    caller_level = caller_level + 1)
  File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 935, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "scipy\setup.py", line 15, in configuration
    config.add_subpackage('linalg')
  File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 1029, in add_subpackage
    caller_level = 2)
  File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 998, in get_subpackage
    caller_level = caller_level + 1)
  File "c:\users\zill-e-huma\appdata\local\programs\python\python35\lib\site-packages\numpy\distutils\misc_util.py", line 935, in _get_configuration_from_setup_py
    config = setup_module.configuration(*args)
  File "scipy\linalg\setup.py", line 20, in configuration
    raise NotFoundError('no lapack/blas resources found')
numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

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

Command "c:\users\zill-e-huma\appdata\local\programs\python\python35\python.exe -u -c "import setuptools, tokenize;file='C:\Users\ZILL-E1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\setup.py';f=getattr(tokenize, 'open', open)(file);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, file, 'exec'))" install --record C:\Users\ZILL-E1\AppData\Local\Temp\pip-1ofstwft-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\ZILL-E~1\AppData\Local\Temp\pip-build-e5d9p_8s\scipy\

from neuroner.

I was also not able to install BRAT and TensorBoard during the previous installation because the link below when clicked was not working.
BRAT should now be accessible through the web browser at http://127.0.0.1:8001.

I would be thankful for your kind support.

from neuroner.

To install scipy, assuming you use python 3.5, you can try:

1. Download scipy‑0.19.0‑cp35‑cp35m‑win_amd64.whl from http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy
2. Open cmd
3. Make sure scipy‑0.19.0‑cp35‑cp35m‑win_amd64.whl is in cmd's current directory, then type pip install scipy‑0.19.0‑cp35‑cp35m‑win_amd64.whl.

Another solution is to use Anaconda, which is a python distribution that comes with many packages including scipy.

I was also not able to install BRAT and TensorBoard during the previous installation because the link below when clicked was not working.

Before visiting http://127.0.0.1:8001 did you try installing BRAT?

from neuroner.

Sorry for bothering you again and again but i am stuck with the installation again as i am new to python....
Thanks for the steps i have followed them and installed every thing except brat up till now while installing brat:
mkdir brat
cd brat
wget http://weaver.nlplab.org/~brat/releases/brat-v1.3_Crunchy_Frog.tar.gz
tar xzf brat-v1.3_Crunchy_Frog.tar.gz
cd brat-v1.3_Crunchy_Frog
./install.sh -u
All these worked fine for me but
executing python standalone.py gave the following error

Zill-E-Huma@Haier-PC ~/brat/brat-v1.3_Crunchy_Frog
$ python standalone.py
File "standalone.py", line 257
except SystemExit, sts:
^
SyntaxError: invalid syntax

The script is stuck at line 257, I cant find the problem kindly suggest some solution.

from neuroner.

Could you please run python --version? I suspect cygwin now comes with python 3, whereas BRAT needs 2.7.

from neuroner.

Sir i have run that command and the version is
$ python --version
Python 3.5.2
That is the version that i have installed following https://github.com/FranckDernoncourt/NeuroNER/blob/master/install_windows.md
as TensorFlow currently supports only Python 3.5. So what should i do now is there any solution?

from neuroner.

For BRAT, all the commands should be run inside the cygwin terminal. As a side note, you don't have to use BRAT to be able to run NeuroNER. BRAT is only needed to easily create, change or view the annotations.

from neuroner.

You're welcome :-) Could you please create a new issue for each question you asked in your previous two messages?

from neuroner.

Thanks!

from neuroner.