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cytoscape / ipycytoscape

A Cytoscape Jupyter widget
https://ipycytoscape.readthedocs.io/en/master/
BSD 3-Clause "New" or "Revised" License
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CytoscapeWidget not rendering #217

Closed 7beggars closed 3 years ago

7beggars commented 3 years ago

Hi,

I'm running the file HTML interaction with graph.ipynb inside jupyter lab but my exit from the line cytoscapeobj it is as below in the figure. What am I doing wrong?

image

ianhi commented 3 years ago

Hi @yaacovNaNachRabbeinu can you specify what versions you are using? This will help determine if you've found a bug or if something is broken about your install

Version Info

7beggars commented 3 years ago

Hi @ianhi here versions:

Version Info

ipycytoscape version (import ipycytoscape; print(ipycytoscape.__version__)) : 1.1.0
Python version: 3.9
Jupyter(Lab) version: 2.2.6

Thanks!

ianhi commented 3 years ago

Argh the proper install instructions still aren't rendering properly on the docs, sorry about that.

Can you try running this command:

jupyter labextension install @jupyter-widgets/jupyterlab-manager
ianhi commented 3 years ago

and then restart your jupyterlab and see if that fixes the issue?

ianhi commented 3 years ago

Full instructions on jlab usage are here: https://github.com/QuantStack/ipycytoscape#for-jupyterlab-users

ianhi commented 3 years ago

Ah yes. That's something we'll need to fix in the documentation as well. You got caught by the transition to JupyterLab 3 which is happening all across the ecosystem right now. Ipycytoscape will support jupyterlab 3 soon, and that will make installation significantly easier. Until then I think the command you need is:

jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0

in order to capture the version for jupyterlab 2.x

Edit: I just updated the readme to reflect this https://github.com/QuantStack/ipycytoscape/commit/8c864668d928d0b0ca2694cdb3cc7c9867b24c77

7beggars commented 3 years ago

Ah yes. That's something we'll need to fix in the documentation as well. You got caught by the transition to JupyterLab 3 which is happening all across the ecosystem right now. Ipycytoscape will support jupyterlab 3 soon, and that will make installation significantly easier. Until then I think the command you need is:

jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0

in order to capture the version for jupyterlab 2.x

Edit: I just updated the readme to reflect this 8c86466

When doing jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0 I get the following error message:

(base) #jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0
An error occured.
ValueError: Please install nodejs >=10.0.0 before continuing. nodejs may be installed using conda or directly from the nodejs website.
See the log file for details:  /tmp/jupyterlab-debug-6hy6k7wf.log
(base) #
marimeireles commented 3 years ago

Are you using a nodejs>=10? You can check it with conda list | grep node if you're using conda.

7beggars commented 3 years ago

conda list | grep node

(base) #conda list | grep node nodejs 6.13.1 0 conda-forge

but when I do `node -v `in my shell terminal:

node -v

v14.15.3



P.S.: i found a similar problem but i use arch linux https://stackoverflow.com/questions/61888748/extension-installation-error-please-install-nodejs-5-and-npm-before-continuing
7beggars commented 3 years ago

I managed to installjupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0 , I tried several solutions to update nodejs via conda and after a while of trying it was successful, but now the following message appears as in the figure below:

image

7beggars commented 3 years ago

Are you using a nodejs>=10? You can check it with conda list | grep node if you're using conda.

I already did several ways to update but the output to conda list | grep node remains:

nodejs 0.1.1 pypi_0 pypi

ianhi commented 3 years ago

@yaacovNaNachRabbeinu what is the output of jupyter labextension list also, have you tried restarted jupyterlab and then re-running all the cells?

Sometimes conda can get kind of stuck, I'd recommend just creating a new environment. Here's a stripped down version that should work (it also uses mamba which is like conda but faster :))

conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0
ianhi commented 3 years ago

Also it's worth mentioning that we will be releasing jlab3 support soon which happily will not require all this mucking around with nodejs and build steps

7beggars commented 3 years ago

jupyter labextension list

I restarted jupyterlab before running the cells. There is an example where loading widgets appears, but it never leaves this message, see the photo below:

image

7beggars commented 3 years ago

@yaacovNaNachRabbeinu what is the output of jupyter labextension list also, have you tried restarted jupyterlab and then re-running all the cells?

Sometimes conda can get kind of stuck, I'd recommend just creating a new environment. Here's a stripped down version that should work (it also uses mamba which is like conda but faster :))

conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0

I will try these guidelines

7beggars commented 3 years ago

jupyter labextension list

my output to jupyter labextension list bellow:


(base) #jupyter labextension list
Fail to get yarn configuration. 
Fail to get yarn configuration. 
JupyterLab v2.2.6
Known labextensions:
   app dir: /opt/anaconda/share/jupyter/lab
        @jupyter-widgets/jupyterlab-manager v2.0.0  enabled  OK
(base) #
7beggars commented 3 years ago

@yaacovNaNachRabbeinu what is the output of jupyter labextension list also, have you tried restarted jupyterlab and then re-running all the cells?

Sometimes conda can get kind of stuck, I'd recommend just creating a new environment. Here's a stripped down version that should work (it also uses mamba which is like conda but faster :))

conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0

when executing the above commands I got a conflict error:


Preparing transaction: done
Verifying transaction: done
Executing transaction: - Enabling notebook extension jupyter-js-widgets/extension...
      - Validating: OK

done
An error occured.
ValueError: 
"@jupyter-widgets/jupyterlab-manager@2.0.0" is not compatible with the current JupyterLab
Conflicting Dependencies:
JupyterLab                        Extension      Package
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/application
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/logconsole
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/mainmenu
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/notebook
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/rendermime
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/rendermime-interfaces
>=6.0.0 <6.1.0                    >=5.0.0 <6.0.0 @jupyterlab/services
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/settingregistry
See the log file for details:  /tmp/jupyterlab-debug-cf9sw_qu.log
(cytoscape) #

here content from log:

Node v15.3.0

Yarn configuration loaded.
> /home/me/.conda/envs/cytoscape/bin/npm pack @jupyter-widgets/jupyterlab-manager@2.0
npm notice 
npm notice 📦  @jupyter-widgets/jupyterlab-manager@2.0.0
npm notice === Tarball Contents === 
npm notice 1.5kB  LICENSE             
npm notice 2.1kB  README.md           
npm notice 277B   lib/index.d.ts      
npm notice 380B   lib/index.js        
npm notice 6.0kB  lib/manager.d.ts    
npm notice 15.3kB lib/manager.js      
npm notice 1.9kB  lib/output.d.ts     
npm notice 5.3kB  lib/output.js       
npm notice 828B   lib/plugin.d.ts     
npm notice 7.8kB  lib/plugin.js       
npm notice 960B   lib/renderer.d.ts   
npm notice 3.3kB  lib/renderer.js     
npm notice 216B   lib/semvercache.d.ts
npm notice 862B   lib/semvercache.js  
npm notice 2.3kB  package.json        
npm notice 375B   schema/plugin.json  
npm notice === Tarball Details === 
npm notice name:          @jupyter-widgets/jupyterlab-manager          
npm notice version:       2.0.0                                        
npm notice filename:      @jupyter-widgets/jupyterlab-manager-2.0.0.tgz
npm notice package size:  13.3 kB                                      
npm notice unpacked size: 49.4 kB                                      
npm notice shasum:        05ab402833df07aac1ec2c549a1d748b3c303185     
npm notice integrity:     sha512-i+qtbEe//W9Ru[...]Fu0KbkxM9aQXQ==     
npm notice total files:   16                                           
npm notice 
jupyter-widgets-jupyterlab-manager-2.0.0.tgz

Traceback (most recent call last):

  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/debuglog.py", line 47, in debug_logging
    yield

  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/labextensions.py", line 127, in start
    ans = self.run_task()

  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/labextensions.py", line 166, in run_task
    return any([

  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/labextensions.py", line 167, in <listcomp>
    install_extension(

  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/commands.py", line 392, in install_extension
    return handler.install_extension(extension, pin=pin)

  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/commands.py", line 614, in install_extension
    info = self._install_extension(extension, tempdir, pin=pin)

  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/commands.py", line 1677, in _install_extension
    raise ValueError(msg)

ValueError: 
"@jupyter-widgets/jupyterlab-manager@2.0.0" is not compatible with the current JupyterLab
Conflicting Dependencies:
JupyterLab                        Extension      Package
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/application
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/logconsole
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/mainmenu
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/notebook
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/rendermime
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/rendermime-interfaces
>=6.0.0 <6.1.0                    >=5.0.0 <6.0.0 @jupyterlab/services
>=3.0.0 <3.1.0                    >=2.0.0 <3.0.0 @jupyterlab/settingregistry

Exiting application: lab
ianhi commented 3 years ago

oops sorry. Need o specify jlab =2.

conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab=2
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0

I'm working on releasing jlab3 support right now, so hopefully that will be the miracle cure :)

7beggars commented 3 years ago

oops sorry. Need o specify jlab =2.

conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab=2
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0

I'm working on releasing jlab3 support right now, so hopefully that will be the miracle cure :)

Now it worked! I haven't finished testing all the examples in the repository, for now, and only one of the examples I tested didn't render, but I'll look at what happened and post if necessary ... But most of the examples in the repository that I've tested so far don't gave no error and rendered perfectly.

Thank you very much!, ThankxXD!! Thanks for your patience.

One of the examples that rendered in the figure below:

image

EDIT UPDATE: give me a day to do tests and definitely take this issue as resolved. Although most errors are due to ignorance of the compatibility dynamics of each component of the repository.

7beggars commented 3 years ago

conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba conda activate cytoscape mamba install -c conda-forge nodejs ipycytoscape jupyterlab=2 jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0

I turned off the PC and when I turned it on again I immediately opened the conda and did a jupyter lab inside the conda shell and now the error model not found ou loading widgets (but never carries) appears again. Apparently the changes did not remain, what should I do so that the changes persist?

marimeireles commented 3 years ago

Hey thanks for posting clear steps of how to reproduce @yaacovNaNachRabbeinu. I'm gonna have a look right now.

marimeireles commented 3 years ago

Hi @yaacovNaNachRabbeinu I've repeated your steps and can't reproduce this error. The only difference is that I didn't specify -c Ananconda as a channel. Maybe it's pulling some packages out of anaconda that don't interact well with the conda forge ones? Really can't think of anything else. Please try again but this time specifying only the -c conda-forge command.

ianhi commented 3 years ago

To clarify: Is that error only there when you open the notebook, but then goes away once you run the cells again? Or is the error also present when you re-run the cells?

7beggars commented 3 years ago

To clarify: Is that error only there when you open the notebook, but then goes away once you run the cells again? Or is the error also present when you re-run the cells?

I'm sorry, I use a 'notebook computer', I forgot to make this clear, replace it now with the word 'PC'. About your doubts: regardless of restarting jupyter lab or not, the error persists in the execution of the cells at all times;

7beggars commented 3 years ago

Hi @yaacovNaNachRabbeinu I've repeated your steps and can't reproduce this error. The only difference is that I didn't specify -c Ananconda as a channel. Maybe it's pulling some packages out of anaconda that don't interact well with the conda forge ones? Really can't think of anything else. Please try again but this time specifying only the -c conda-forge command.

I will redo the execution, although I have tried to correct this by running the commands below again before seeing your request for clarification, follow the complete execution of the commands below, but I imagine I should have activated the environment by doing conda activate, maybe that's it, I will check:

#source /opt/anaconda/bin/activate root
(base) #conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab=2
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0
WARNING: A directory already exists at the target location '/home/me/.conda/envs/cytoscape'
but it is not a conda environment.
Continue creating environment (y/[n])? n

CondaSystemExit: Exiting.

^CTraceback (most recent call last):
  File "/home/me/.conda/envs/cytoscape/bin/mamba", line 7, in <module>
    from mamba.mamba import main
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/mamba/mamba.py", line 52, in <module>
    import mamba.mamba_api as api
ImportError: KeyboardInterrupt: 
^CTraceback (most recent call last):
  File "/home/me/.conda/envs/cytoscape/bin/jupyter-labextension", line 6, in <module>
    from jupyterlab.labextensions import main
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/labextensions.py", line 16, in <module>
    from .commands import (
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/commands.py", line 29, in <module>
    from jupyterlab_server.process import which, Process, WatchHelper, list2cmdline
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab_server/__init__.py", line 4, in <module>
    from .app import LabServerApp
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab_server/app.py", line 9, in <module>
    from .server import ServerApp
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab_server/server.py", line 20, in <module>
    from notebook.notebookapp import aliases, flags, NotebookApp as ServerApp
  File "/home/me/.local/lib/python3.9/site-packages/notebook/notebookapp.py", line 49, in <module>
    from zmq.eventloop import ioloop
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/zmq/eventloop/__init__.py", line 3, in <module>
    from zmq.eventloop.ioloop import IOLoop
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/zmq/eventloop/ioloop.py", line 78, in <module>
    while _IOLoop.configurable_default() is not _IOLoop:
  File "/home/me/.local/lib/python3.9/site-packages/tornado/ioloop.py", line 326, in configurable_default
    from tornado.platform.asyncio import AsyncIOLoop
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 786, in exec_module
  File "<frozen importlib._bootstrap_external>", line 881, in get_code
  File "<frozen importlib._bootstrap_external>", line 980, in get_data
KeyboardInterrupt

(cytoscape) #conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab=2
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0
WARNING: A directory already exists at the target location '/home/me/.conda/envs/cytoscape'
but it is not a conda environment.
Continue creating environment (y/[n])? y

CondaValueError: prefix already exists: /home/me/.conda/envs/cytoscape

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.7.6) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

NoBaseEnvironmentError: This conda installation has no default base environment. Use
'conda create' to create new environments and 'conda activate' to
activate environments.

Building jupyterlab assets (build:prod:minimize)
(cytoscape) #
marimeireles commented 3 years ago

Hm, I'm a bit confused by your log but it seems like you're copy/pasting all lines at once? Run them line by line instead. Also, I recommend changing the name of the environment, because there's already an environment called cytoscape.

7beggars commented 3 years ago

Hi @yaacovNaNachRabbeinu I've repeated your steps and can't reproduce this error. The only difference is that I didn't specify -c Ananconda as a channel. Maybe it's pulling some packages out of anaconda that don't interact well with the conda forge ones? Really can't think of anything else. Please try again but this time specifying only the -c conda-forge command.

I will redo the execution, although I have tried to correct this by running the commands below again before seeing your request for clarification, follow the complete execution of the commands below, but I imagine I should have activated the environment by doing conda activate, maybe that's it, I will check:

#source /opt/anaconda/bin/activate root
(base) #conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab=2
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0
WARNING: A directory already exists at the target location '/home/me/.conda/envs/cytoscape'
but it is not a conda environment.
Continue creating environment (y/[n])? n

CondaSystemExit: Exiting.

^CTraceback (most recent call last):
  File "/home/me/.conda/envs/cytoscape/bin/mamba", line 7, in <module>
    from mamba.mamba import main
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/mamba/mamba.py", line 52, in <module>
    import mamba.mamba_api as api
ImportError: KeyboardInterrupt: 
^CTraceback (most recent call last):
  File "/home/me/.conda/envs/cytoscape/bin/jupyter-labextension", line 6, in <module>
    from jupyterlab.labextensions import main
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/labextensions.py", line 16, in <module>
    from .commands import (
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab/commands.py", line 29, in <module>
    from jupyterlab_server.process import which, Process, WatchHelper, list2cmdline
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab_server/__init__.py", line 4, in <module>
    from .app import LabServerApp
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab_server/app.py", line 9, in <module>
    from .server import ServerApp
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/jupyterlab_server/server.py", line 20, in <module>
    from notebook.notebookapp import aliases, flags, NotebookApp as ServerApp
  File "/home/me/.local/lib/python3.9/site-packages/notebook/notebookapp.py", line 49, in <module>
    from zmq.eventloop import ioloop
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/zmq/eventloop/__init__.py", line 3, in <module>
    from zmq.eventloop.ioloop import IOLoop
  File "/home/me/.conda/envs/cytoscape/lib/python3.9/site-packages/zmq/eventloop/ioloop.py", line 78, in <module>
    while _IOLoop.configurable_default() is not _IOLoop:
  File "/home/me/.local/lib/python3.9/site-packages/tornado/ioloop.py", line 326, in configurable_default
    from tornado.platform.asyncio import AsyncIOLoop
  File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
  File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 786, in exec_module
  File "<frozen importlib._bootstrap_external>", line 881, in get_code
  File "<frozen importlib._bootstrap_external>", line 980, in get_data
KeyboardInterrupt

(cytoscape) #conda create -n cytoscape -c conda-forge -c anaconda python=3 mamba
conda activate cytoscape
mamba install -c conda-forge nodejs ipycytoscape jupyterlab=2
jupyter labextension install @jupyter-widgets/jupyterlab-manager@2.0
WARNING: A directory already exists at the target location '/home/me/.conda/envs/cytoscape'
but it is not a conda environment.
Continue creating environment (y/[n])? y

CondaValueError: prefix already exists: /home/me/.conda/envs/cytoscape

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
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        mamba (0.7.6) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
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NoBaseEnvironmentError: This conda installation has no default base environment. Use
'conda create' to create new environments and 'conda activate' to
activate environments.

Building jupyterlab assets (build:prod:minimize)
(cytoscape) #

I ran jupyter lab and the error continues, I will try to activate the conda environment before running jupyter lab:

image

7beggars commented 3 years ago

Hm, I'm a bit confused by your log but it seems like you're copy/pasting all lines at once? Run them line by line instead. Also, I recommend changing the name of the environment, because there's already an environment called cytoscape.

I'll do as I said, but yes, I'm running one line at a time of code.

7beggars commented 3 years ago

Hi @yaacovNaNachRabbeinu I've repeated your steps and can't reproduce this error. The only difference is that I didn't specify -c Ananconda as a channel. Maybe it's pulling some packages out of anaconda that don't interact well with the conda forge ones? Really can't think of anything else. Please try again but this time specifying only the -c conda-forge command.

Now it worked, the point is that I didn't really do conda activate cytoscape. Although I also think to follow your advice and avoid using -c anaconda. Thank you very much, I am closing the issue as resolved, if you allow me. @marimeireles and @ianhi you were amazing! Thank*^2xD!

marimeireles commented 3 years ago

No problem, glad you found your way =) It's a lot of little things to keep track of.