Issue with dependencies (version `CXXABI_1.3.8' not found)

[marianaql]

Dear SCALE team,

I am currently trying to run SCALE, which has been successfully installed. However, it outputs the following error regarding version `CXXABI_1.3.8' not found by sklearn package (which is already updated), and I was wondering if you could help me with this. Thank you very much in advance!

(base) [mq224@login-e-14 SCALE]$ python SCALE.py -d ../files/ -k 4 --impute Traceback (most recent call last): File "SCALE.py", line 25, in from scale import SCALE File "/rds/project/bg200/rds-bg200-hphi-gottgens/users/mq224/project_atacseq/samples/Fernando/SLX18781_SINAB12/outs/cellRangerPeaks/SCALExscATACseq/SCALE/scale/init.py", line 16, in from .model import * File "/rds/project/bg200/rds-bg200-hphi-gottgens/users/mq224/project_atacseq/samples/Fernando/SLX18781_SINAB12/outs/cellRangerPeaks/SCALExscATACseq/SCALE/scale/model.py", line 22, in from sklearn.mixture import GaussianMixture File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/mixture/init.py", line 5, in from .gaussian_mixture import GaussianMixture File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/mixture/gaussian_mixture.py", line 11, in from .base import BaseMixture, _check_shape File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/mixture/base.py", line 13, in from .. import cluster File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/cluster/init.py", line 6, in from .spectral import spectral_clustering, SpectralClustering File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/cluster/spectral.py", line 16, in from ..neighbors import kneighbors_graph File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/neighbors/init.py", line 16, in from .nca import NeighborhoodComponentsAnalysis File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/neighbors/nca.py", line 22, in from ..decomposition import PCA File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/decomposition/init.py", line 11, in from .sparse_pca import SparsePCA, MiniBatchSparsePCA File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/decomposition/sparse_pca.py", line 11, in from ..linear_model import ridge_regression File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/linear_model/init.py", line 26, in from .logistic import (LogisticRegression, LogisticRegressionCV, File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/linear_model/logistic.py", line 23, in from ..svm.base import _fit_liblinear File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/svm/init.py", line 13, in from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC,
File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/svm/classes.py", line 4, in from .base import _fit_liblinear, BaseSVC, BaseLibSVM File "/home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/svm/base.py", line 6, in from . import libsvm, liblinear ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /home/mq224/anaconda3/install/lib/python3.7/site-packages/sklearn/svm/libsvm.cpython-37m-x86_64-linux-gnu.so)

[jsxlei]

It seems that your environment settings are incompatible with sklearn. You can setup a new python env via conda, then install SCALE conda create -n SCALE python=3.6 pytorch conda activate SCALE

git clone git://github.com/jsxlei/SCALE.git cd SCALE python setup.py install