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jamescasbon / PyVCF

A Variant Call Format reader for Python.
http://pyvcf.readthedocs.org/en/latest/index.html
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import error #339

Open gebdu opened 2 years ago

gebdu commented 2 years ago

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