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import error #2

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joy1314 opened this Issue Apr 21, 2017 · 4 comments

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@joy1314

joy1314 commented Apr 21, 2017

when I have installed this and I typed "from spice import featext"
It shows the error like this ,
Traceback (most recent call last):
File "", line 1, in
File "/usr/local/lib/python2.7/dist-packages/spice/featext.py", line 14, in
from spice import featmat
File "/usr/local/lib/python2.7/dist-packages/spice/featmat.py", line 21, in
sys.path.insert(1, os.environ['SKL'])
File "/usr/lib/python2.7/UserDict.py", line 40, in getitem
raise KeyError(key)
KeyError: 'SKL'

Do you know why?How to fix it?

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basvandenberg Apr 21, 2017

Owner

Hi @joy1314,

Thanks for posting this issue. I updated the software, and with the latest version you should not get this error anymore.

To install spice, make sure to have the following required software installed (the commands below are for a debian-based linux system):

sudo apt install python-tk
pip install --user numpy scipy matplotlib sklearn prody

To be sure, remove your current biopy and spice installations:

cd /usr/local/lib/python2.7/dist-packages
sudo rm -rf spice
sudo rm SPiCE-*
sudo rm -rf biopy
sudo rm biopy-*
cd /usr/local/bin
sudo rm classification classify featext job_runner

And then install the latest biopy and spice:

cd ~/Downloads
wget https://github.com/basvandenberg/biopy/archive/develop.zip
unzip develop.zip
cd biopy-develop
sudo python setup.py install
cd ~/Downloads
wget https://github.com/basvandenberg/spice/archive/master.zip
unzip master.zip
cd spice-master
sudo python setup.py install
cd ~/Downloads
rm develop.zip
rm master.zip
rm -rf biopy-develop
rm -rf spice-master

I hope this works for you. This software is developed some time ago and not maintained since. Please let me know if something is not working properly or if you need more help.

Owner

basvandenberg commented Apr 21, 2017

Hi @joy1314,

Thanks for posting this issue. I updated the software, and with the latest version you should not get this error anymore.

To install spice, make sure to have the following required software installed (the commands below are for a debian-based linux system):

sudo apt install python-tk
pip install --user numpy scipy matplotlib sklearn prody

To be sure, remove your current biopy and spice installations:

cd /usr/local/lib/python2.7/dist-packages
sudo rm -rf spice
sudo rm SPiCE-*
sudo rm -rf biopy
sudo rm biopy-*
cd /usr/local/bin
sudo rm classification classify featext job_runner

And then install the latest biopy and spice:

cd ~/Downloads
wget https://github.com/basvandenberg/biopy/archive/develop.zip
unzip develop.zip
cd biopy-develop
sudo python setup.py install
cd ~/Downloads
wget https://github.com/basvandenberg/spice/archive/master.zip
unzip master.zip
cd spice-master
sudo python setup.py install
cd ~/Downloads
rm develop.zip
rm master.zip
rm -rf biopy-develop
rm -rf spice-master

I hope this works for you. This software is developed some time ago and not maintained since. Please let me know if something is not working properly or if you need more help.

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joy1314 Apr 23, 2017

Thanks ,it works .But I have another question. I can not open http://helix.ewi.tudelft.nl/spice .what is the matter?How to fix it ??
Looking forward to your reply
Thank you very much. @basvandenberg

joy1314 commented Apr 23, 2017

Thanks ,it works .But I have another question. I can not open http://helix.ewi.tudelft.nl/spice .what is the matter?How to fix it ??
Looking forward to your reply
Thank you very much. @basvandenberg

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joy1314 Apr 23, 2017

@basvandenberg Now I have another problem
When I typeclassification and classifyon the command line .It shows the error like this
Traceback (most recent call last): File "/usr/local/bin/classification", line 16, in <module> sys.path.insert(1, os.environ['SKL']) File "/usr/lib/python2.7/UserDict.py", line 40, in __getitem__ raise KeyError(key) KeyError: 'SKL'

Traceback (most recent call last): File "/usr/local/bin/classify", line 5, in <module> from spice.classify import classify File "/usr/local/lib/python2.7/dist-packages/spice/classify.py", line 9, in <module> sys.path.insert(1, os.environ['SKL']) File "/usr/lib/python2.7/UserDict.py", line 40, in __getitem__ raise KeyError(key) KeyError: 'SKL'
How to fix them?
Thank you very much

joy1314 commented Apr 23, 2017

@basvandenberg Now I have another problem
When I typeclassification and classifyon the command line .It shows the error like this
Traceback (most recent call last): File "/usr/local/bin/classification", line 16, in <module> sys.path.insert(1, os.environ['SKL']) File "/usr/lib/python2.7/UserDict.py", line 40, in __getitem__ raise KeyError(key) KeyError: 'SKL'

Traceback (most recent call last): File "/usr/local/bin/classify", line 5, in <module> from spice.classify import classify File "/usr/local/lib/python2.7/dist-packages/spice/classify.py", line 9, in <module> sys.path.insert(1, os.environ['SKL']) File "/usr/lib/python2.7/UserDict.py", line 40, in __getitem__ raise KeyError(key) KeyError: 'SKL'
How to fix them?
Thank you very much

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joy1314 Apr 27, 2017

thank you very much @basvandenberg

joy1314 commented Apr 27, 2017

thank you very much @basvandenberg

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