jsxlei
commented
4 years ago 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
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)