Load time error - Githubissues

abmmki commented 2 years ago

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.

jon-xu commented 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

abmmki commented 2 years ago

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