Issue on clustering after changing the pip installation and trying conda installation

[andresilvapimentel]

I have used pyemma with no issue for over a year installing it on google colab with: pip install wheel pip install pyemma

Suddenly, it stopped working last week. I do not know why. I found the following issue:

Building wheels for collected packages: pyemma Building wheel for pyemma (PEP 517) ... error ERROR: Failed building wheel for pyemma Failed to build pyemma ERROR: Could not build wheels for pyemma which use PEP 517 and cannot be installed directly

Then, I tried to install it by using the conda package on google colab bu using the following:

! wget https://repo.anaconda.com/miniconda/Miniconda3-py37_4.8.2-Linux-x86_64.sh ! chmod +x Miniconda3-py37_4.8.2-Linux-x86_64.sh ! bash ./Miniconda3-py37_4.8.2-Linux-x86_64.sh -b -f -p /usr/local import sys sys.path.append('/usr/local/lib/python3.7/site-packages/')

!curl -s https://raw.githubusercontent.com/markovmodel/PyEMMA/devel/install_miniconda%2Bpyemma.sh | bash !conda install -c conda-forge pyemma

It works pretty well until clustering. I found the following using: cluster = pyemma.coordinates.cluster_kmeans(tica_output, k=k, max_iter=50, stride=50)

/usr/local/lib/python3.7/site-packages/deeptime/data/_pbf_simulator.py in () 3 from threadpoolctl import threadpool_limits 4 ----> 5 from . import _data_bindings as bd 6 from ..util.decorators import plotting_function 7 from ..util.parallel import handle_n_jobs, joining

ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /usr/local/lib/python3.7/site-packages/deeptime/data/_data_bindings.cpython-37m-x86_64-linux-gnu.so)

Please, let me know what is going on. hanks.

[clonker]

We probably have to do a patch-release of pyemma. In the meantime you can try this: !pip install git+https://github.com/markovmodel/pyemma.git@devel

[clonker]

patch is out, would you mind trying if everything works for you now? the pyemma version you are looking for is 2.5.10.