Closed abmmki closed 2 years ago
scSplit doesn't use any R package.
Please test in your platform all the below python modules can be imported properly:
import numpy as np import pysam as ps import pandas as pd import statistics as stat from scipy.stats import binom from scipy.sparse import csr_matrix from sklearn.cluster import KMeans from sklearn.decomposition import PCA from sklearn.preprocessing import StandardScaler import sys, io, vcf, csv, math, datetime, pickle, argparse
Hi,
It is the module vcf that is creating problem. It installed successfully:
pip3 install PyVCF
Then we import vcf module in python (removing and reinstalling did not solve the problem):
python3 Python 3.7.7 (default, Mar 13 2020, 21:39:43) [GCC 9.2.1 20190827 (Red Hat 9.2.1-1)] on linux Type "help", "copyright", "credits" or "license" for more information.
import vcf R[write to console]: Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/methods/libs/methods.so': /usr/local/lib64/R/library/methods/libs/methods.so: undefined symbol: Rf_allocS4Object
R[write to console]: Error: package or namespace load failed for ‘utils’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/utils/libs/utils.so': /usr/local/lib64/R/library/utils/libs/utils.so: undefined symbol: R_NilValue
R[write to console]: Error: package or namespace load failed for ‘grDevices’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/grDevices/libs/grDevices.so': /usr/local/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: R_NilValue
R[write to console]: Error: package or namespace load failed for ‘graphics’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/grDevices/libs/grDevices.so': /usr/local/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: R_NilValue
R[write to console]: Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/grDevices/libs/grDevices.so': /usr/local/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: R_NilValue
R[write to console]: Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/methods/libs/methods.so': /usr/local/lib64/R/library/methods/libs/methods.so: undefined symbol: Rf_allocS4Object
R[write to console]: During startup - R[write to console]: Warning messages:
R[write to console]: 1: package "methods" in options("defaultPackages") was not found
R[write to console]: 2: package ‘utils’ in options("defaultPackages") was not found
R[write to console]: 3: package ‘grDevices’ in options("defaultPackages") was not found
R[write to console]: 4: package ‘graphics’ in options("defaultPackages") was not found
R[write to console]: 5: package ‘stats’ in options("defaultPackages") was not found
R[write to console]: 6: package ‘methods’ in options("defaultPackages") was not found
R[write to console]: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib64/R/library/methods/libs/methods.so': /usr/local/lib64/R/library/methods/libs/methods.so: undefined symbol: Rf_allocS4Object
Thanks for the update! In this case, I would think the best is to check with PyVCF team. Hope it will be resolved soon!
scSplit -h
R[write to console]: Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/methods/libs/methods.so': /usr/local/lib64/R/library/methods/libs/methods.so: undefined symbol: Rf_allocS4Object
R[write to console]: Error: package or namespace load failed for ‘utils’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/utils/libs/utils.so': /usr/local/lib64/R/library/utils/libs/utils.so: undefined symbol: R_NilValue
R[write to console]: Error: package or namespace load failed for ‘grDevices’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/grDevices/libs/grDevices.so': /usr/local/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: R_NilValue
R[write to console]: Error: package or namespace load failed for ‘graphics’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/grDevices/libs/grDevices.so': /usr/local/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: R_NilValue
R[write to console]: Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/grDevices/libs/grDevices.so': /usr/local/lib64/R/library/grDevices/libs/grDevices.so: undefined symbol: R_NilValue
R[write to console]: Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/usr/local/lib64/R/library/methods/libs/methods.so': /usr/local/lib64/R/library/methods/libs/methods.so: undefined symbol: Rf_allocS4Object
R[write to console]: During startup - R[write to console]: Warning messages:
R[write to console]: 1: package "methods" in options("defaultPackages") was not found
R[write to console]: 2: package ‘utils’ in options("defaultPackages") was not found
R[write to console]: 3: package ‘grDevices’ in options("defaultPackages") was not found
R[write to console]: 4: package ‘graphics’ in options("defaultPackages") was not found
R[write to console]: 5: package ‘stats’ in options("defaultPackages") was not found
R[write to console]: 6: package ‘methods’ in options("defaultPackages") was not found
R[write to console]: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/usr/local/lib64/R/library/methods/libs/methods.so': /usr/local/lib64/R/library/methods/libs/methods.so: undefined symbol: Rf_allocS4Object
usage: scSplit []
Commands: count Generate REF/ALT count matrices from pooled BAM file run Demultiplex the scRNA-Seq using REF/ALT count matrices genotype Generate sample genotypes in VCF format
How to solve this? Using Fedora, Python 3.6. All python module installed. Also all R packages.