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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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Stream Installation, it hangs in solving environment #77

Closed linwang6 closed 4 years ago

linwang6 commented 4 years ago

Hi, Thanks for this cool tool. When I tried to install stream,

conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda create -n env_stream python stream jupyter Solving environment: /

it hangs in solving environment step, how to fix this? Any advice?

Thanks in advance.

huidongchen commented 4 years ago

Yeah, conda install usually does take some time. But just in case it gets stuck, can you specify stream version and give it try again? something like conda create -n env_stream python stream=1.0 jupyter?

linwang6 commented 4 years ago

Thanks huidong, I will have a try.

linwang6 commented 4 years ago

Hi huidong, When I tried "conda create -n stream python stream=1.0 jupyter", it solved the solving environment step, but it gave a new error information, see below, ............... Preparing transaction: done Verifying transaction: done Executing transaction: failed ERROR conda.core.link:_execute(481): An error occurred while installing package 'conda-forge::attrs-19.3.0-py_0'. FileNotFoundError(2, "No such file or directory: '/Users/lwang/miniconda3/envs/SCstream/bin/python3.7'") Attempting to roll back.

Rolling back transaction: done

FileNotFoundError(2, "No such file or directory: '/Users/lwang/miniconda3/envs/SCstream/bin/python3.7'")

Any suggestions? Thanks in advance.

lucapinello commented 4 years ago

It seems a more general problem with conda and not STREAM, see here: https://github.com/conda/conda/issues/8051

Which version of conda are you using? and are you on Mac?

You could try:

conda create -n stream-env python=3.7 conda activate stream-env conda install stream=1.0 jupyter

Please keep us posted.

On Wed, Jun 10, 2020 at 11:19 PM linwang6 notifications@github.com wrote:

Hi huidong, When I tried "conda create -n stream python stream=1.0 jupyter", it solved the solving environment step, but it gave a new error information, see below, ............... Preparing transaction: done Verifying transaction: done Executing transaction: failed ERROR conda.core.link:_execute(481): An error occurred while installing package 'conda-forge::attrs-19.3.0-py_0'. FileNotFoundError(2, "No such file or directory: '/Users/lwang/miniconda3/envs/SCstream/bin/python3.7'") Attempting to roll back.

Rolling back transaction: done

FileNotFoundError(2, "No such file or directory: '/Users/lwang/miniconda3/envs/SCstream/bin/python3.7'")

Any suggestions? Thanks in advance.

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linwang6 commented 4 years ago

Thanks Luca, I'm using conda 4.4.10. Right, I'm on Mac. I will try this and update you.

linwang6 commented 4 years ago

Hi Luca, It works using your suggested command lines, and it's installed without any error. But when I import stream, it gives me segmentation fault 11, see below,

(stream) wanglin@Wangs-Mac:/Users/wanglin$ python

Python 3.7.6 | packaged by conda-forge | (default, Jun 1 2020, 18:33:30) [Clang 9.0.1 ] on darwin Type "help", "copyright", "credits" or "license" for more information.

import stream as st cannot find system Renviron /Users/wanglin/miniconda3/envs/stream/lib/python3.7/site-packages/rpy2/rinterface/init.py:146: RRuntimeWarning: Fatal error: unable to open the base package

warnings.warn(x, RRuntimeWarning) Segmentation fault: 11

That means it not find Renviron, how should I set it? Thanks in advance.

linwang6 commented 4 years ago

Here is the R path $ which R /Users/wanglin/miniconda3/envs/stream/bin/R

lucapinello commented 4 years ago

This is probably still a bug of the old conda version. Try to update to the latest version i.e. 4.8 and potentially consider reinstalling miniconda from scratch.

On Thu, Jun 11, 2020 at 12:14 PM linwang6 notifications@github.com wrote:

Here is the R path $ which R /Users/wanglin/miniconda3/envs/stream/bin/R

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linwang6 commented 4 years ago

Got it, I will update conda, and try again. Thanks!

linwang6 commented 4 years ago

I have reinstalled the latest miniconda (https://docs.conda.io/en/latest/miniconda.html), and it still gives the same error,

(stream_env) wanglin@Wangs-MacBook-Pro-2:/Users/wanglin0$ python Python 3.7.6 | packaged by conda-forge | (default, Jun 1 2020, 18:33:30) [Clang 9.0.1 ] on darwin Type "help", "copyright", "credits" or "license" for more information.

import stream as st cannot find system Renviron /Users/wanglin/miniconda3/envs/stream_env/lib/python3.7/site-packages/rpy2/rinterface/init.py:146: RRuntimeWarning: Fatal error: unable to open the base package

warnings.warn(x, RRuntimeWarning) Segmentation fault: 11

Any advices? Thanks so much.

huidongchen commented 4 years ago

It seems that someone else also reported a similar issue previously #24 , but unfortunately I have not been able to reproduce this error myself. Can you share with us your pkg version info, i.e. the output from conda list?

linwang6 commented 4 years ago

Sure, see below,

(stream_env) wanglin@Wangs-MacBook-Pro-2:/Users/wanglin0$ conda list packages in environment at /Users/wanglin/miniconda3/envs/stream_env:

linwang6 commented 4 years ago

And conda info

$conda info

 active environment : stream_env
active env location : /Users/wanglin/miniconda3/envs/stream_env
        shell level : 1
   user config file : /Users/wanglin/.condarc
   populated config files : /Users/wanglin/.condarc
      conda version : 4.8.2
conda-build version : not installed
     python version : 3.7.6.final.0
   virtual packages : __osx=10.12.6
   base environment : /Users/wanglin/miniconda3  (writable)
       channel URLs : https://conda.anaconda.org/conda-forge/osx-64
                      https://conda.anaconda.org/conda-forge/noarch
                      https://conda.anaconda.org/bioconda/osx-64
                      https://conda.anaconda.org/bioconda/noarch
                      https://repo.anaconda.com/pkgs/main/osx-64
                      https://repo.anaconda.com/pkgs/main/noarch
                      https://repo.anaconda.com/pkgs/r/osx-64
                      https://repo.anaconda.com/pkgs/r/noarch
      package cache : /Users/wanglin/miniconda3/pkgs
                      /Users/wanglin/.conda/pkgs
   envs directories : /Users/wanglin/miniconda3/envs
                      /Users/wanglin/.conda/envs
           platform : osx-64
         user-agent : conda/4.8.2 requests/2.22.0 CPython/3.7.6 Darwin/16.7.0 OSX/10.12.6
            UID:GID : 501:20
         netrc file : None
       offline mode : False
huidongchen commented 4 years ago

This seems a notorious rpy2-related issue.. please see this post https://bitbucket.org/rpy2/rpy2/issues/214/segmentation-fault-11-on-mac-os-x-mountain

but someone has revolved it via: https://stackoverflow.com/questions/39347782/getting-segmentation-fault-core-dumped-error-while-importing-robjects-from-rpy2/53639407#53639407

Let me know if this works for you.

linwang6 commented 4 years ago

Thanks Huidong, will have a try.

linwang6 commented 4 years ago

Hi,

Finally it works now. Thanks for your help.

One last question, this command line "st.plot_dimension_reduction(adata,color=['label'],show_graph=False,show_text=False)" works well, but when I add plotly=True (st.plot_dimension_reduction(adata,color=['label'],show_graph=False,show_text=False,plotly=True)), the figure not pop up, it just prints hundred lines like "{'text/html': ' Githubissues.

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