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PrincetonUniversity / DP_GP_cluster

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Unable to install and test DP_GP #4

Closed kanekalla closed 6 years ago

kanekalla commented 6 years ago

Hello team,

I am trying to use DP_GP but having difficult to use it. The recent error that I got is after trying to install python2.7 setup.py install Traceback (most recent call last): File "setup.py", line 2, in from Cython.Distutils import build_ext ImportError: No module named Cython.Distutils

I also tried to run the test plot directly from the bin python2.7 bin/DP_GP_cluster.py -i test/test.txt -o test/test -p png -n 20 --plot Traceback (most recent call last): File "bin/DP_GP_cluster.py", line 24, in from DP_GP import plot ImportError: No module named DP_GP

Can you kindly look into this?

IanMcDowell commented 6 years ago

Please install cython and retry. Let me know the error message

On Wed, Feb 28, 2018 at 8:15 PM, Kishore R. Anekalla < notifications@github.com> wrote:

Hello team,

I am trying to use DP_GP but having difficult to use it. The recent error that I got is after trying to install python2.7 setup.py install Traceback (most recent call last): File "setup.py", line 2, in from Cython.Distutils import build_ext ImportError: No module named Cython.Distutils

I also tried to run the test plot directly from the bin python2.7 bin/DP_GP_cluster.py -i test/test.txt -o test/test -p png -n 20 --plot Traceback (most recent call last): File "bin/DP_GP_cluster.py", line 24, in from DP_GP import plot ImportError: No module named DP_GP

Can you kindly look into this?

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kanekalla commented 6 years ago

Hi Ian,

installed successfully and I am getting scipy.cluster.hierarchy error. Installing output: running install running build running build_py running build_ext skipping 'DP_GP/core.c' Cython extension (up-to-date) skipping 'DP_GP/cluster_tools.c' Cython extension (up-to-date) running build_scripts running install_lib running install_scripts changing mode of /home/kishore/.virtualenvs/iso/bin/DP_GP_cluster.py to 775 running install_egg_info Removing /home/kishore/.virtualenvs/iso/lib/python2.7/site-packages/DP_GP_cluster-0.1-py2.7.egg-info Writing /home/kishore/.virtualenvs/iso/lib/python2.7/site-packages/DP_GP_cluster-0.1-py2.7.egg-info

Error: Traceback (most recent call last): File "/usr/local/bin/DP_GP_cluster.py", line 24, in from DP_GP import plot File "/usr/local/lib/python2.7/dist-packages/DP_GP/plot.py", line 11, in from scipy.cluster.hierarchy import linkage, dendrogram ImportError: No module named scipy.cluster.hierarchy

However, I am able to load scipy.cluster.heirarchy using python CLI Python 2.7.14 (default, Sep 23 2017, 22:06:14) [GCC 7.2.0] on linux2 Type "help", "copyright", "credits" or "license" for more information.

import scipy.cluster.hierarchy

IanMcDowell commented 6 years ago

DPGP has the following requirements:

GPy, pandas, numpy, scipy (>= 0.14), matplotlib.pyplot

Install and retry please.

On Thu, Mar 1, 2018 at 11:09 PM, Kishore R. Anekalla < notifications@github.com> wrote:

Hi Ian,

installed successfully and I am getting scipy.cluster.hierarchy error. Installing output: running install running build running build_py running build_ext skipping 'DP_GP/core.c' Cython extension (up-to-date) skipping 'DP_GP/cluster_tools.c' Cython extension (up-to-date) running build_scripts running install_lib running install_scripts changing mode of /home/kishore/.virtualenvs/iso/bin/DP_GP_cluster.py to 775 running install_egg_info Removing /home/kishore/.virtualenvs/iso/lib/python2.7/site- packages/DP_GP_cluster-0.1-py2.7.egg-info Writing /home/kishore/.virtualenvs/iso/lib/python2.7/site- packages/DP_GP_cluster-0.1-py2.7.egg-info

Error: Traceback (most recent call last): File "/usr/local/bin/DP_GP_cluster.py", line 24, in from DP_GP import plot File "/usr/local/lib/python2.7/dist-packages/DP_GP/plot.py", line 11, in from scipy.cluster.hierarchy import linkage, dendrogram ImportError: No module named scipy.cluster.hierarchy

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kanekalla commented 6 years ago

Hello Ian, I am still unable to test DP_GP.

I have cross checked the versions,

Python 2.7.14 (default, Sep 23 2017, 22:06:14) [GCC 7.2.0] on linux2 Type "help", "copyright", "credits" or "license" for more information.

import GPy import matplotlib import pandas import numpy import scipy print scipy.version 1.0.0 print numpy.version 1.14.1 print GPy.version 1.9.2 print pandas.version 0.22.0 print matplotlib.version 2.1.2 import matplotlib.pyplot print sklearn.version 0.19.1

Error: (iso) kishore@Jaya:~winter1718/rotation/DP_GP_cluster$ DP_GP_cluster.py -i test/test.txt -o test/test -p png -n 20 --plot Traceback (most recent call last): File "/home/kishore/.virtualenvs/iso/bin/DP_GP_cluster.py", line 24, in from DP_GP import plot File "/usr/local/lib/python2.7/dist-packages/DP_GP/plot.py", line 11, in from scipy.cluster.hierarchy import linkage, dendrogram ImportError: No module named scipy.cluster.hierarchy

I am running using virtual environment created using virtualenvwrapper.

IanMcDowell commented 6 years ago

Hmm, that's strange. Try running for yourself:

from scipy.cluster.hierarchy import linkage, dendrogram

If that works, then DPGP is finding a different python than your usual python path.

On Fri, Mar 2, 2018 at 11:02 AM, Kishore R. Anekalla < notifications@github.com> wrote:

Hello Ian, I am still unable to test DP_GP.

I have cross checked the versions,

Python 2.7.14 (default, Sep 23 2017, 22:06:14) [GCC 7.2.0] on linux2 Type "help", "copyright", "credits" or "license" for more information.

import GPy import matplotlib import pandas import numpy import scipy print scipy.version 1.0.0 print numpy.version 1.14.1 print GPy.version 1.9.2 print pandas.version 0.22.0 print matplotlib.version 2.1.2 import matplotlib.pyplot

Error: (iso) kishore@Jaya:~winter1718/rotation/DP_GP_cluster$ DP_GP_cluster.py -i test/test.txt -o test/test -p png -n 20 --plot Traceback (most recent call last): File "/home/kishore/.virtualenvs/iso/bin/DP_GP_cluster.py", line 24, in from DP_GP import plot File "/usr/local/lib/python2.7/dist-packages/DP_GP/plot.py", line 11, in from scipy.cluster.hierarchy import linkage, dendrogram ImportError: No module named scipy.cluster.hierarchy

I am running using virtual environment created using virtualenvwrapper.

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-- Ian McDowell Bioinformatician II Duke University

kanekalla commented 6 years ago

Python 2.7.14 (default, Sep 23 2017, 22:06:14) [GCC 7.2.0] on linux2 Type "help", "copyright", "credits" or "license" for more information.

from scipy.cluster.hierarchy import linkage, dendrogram

This one seems working

kanekalla commented 6 years ago

Hi Ian,

I opted out of virtual environment and running directly and its running now. It might be because of virtual environment its taking different path.

Thanks for your help !!