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collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status #11

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zhang570221322 opened this issue Apr 12, 2022 · 1 comment

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@zhang570221322
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Python2.7 is not support for the biopython.

@zhang570221322
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Then I use the conda install biopython.
my package version is as follows.

biopython      1.70     
certifi        2016.9.26
Cython         0.20.1   
mmtf-python    1.1.2    
msgpack-python 0.4.8    
numpy          1.12.1   
pip            20.0.2   
reportlab      3.2.0    
setuptools     36.4.0   
wheel          0.37.1  

A error occurs.

/data/home/wlzhang/anaconda3/envs/taxonomer/compiler_compat/ld: build/temp.linux-x86_64-2.7/src/query_db.o:/data/home/wlzhang/classfication/software/kraken2/taxonomer_0.5-0.5/taxonomer/src/load_dbs.h:42: multiple definition of `tax_to_seqs'; build/temp.linux-x86_64-2.7/scripts/cython/binner_PY.o:/data/home/wlzhang/classfication/software/kraken2/taxonomer_0.5-0.5/taxonomer/scripts/cython/../../src/load_dbs.h:42: first defined here
/data/home/wlzhang/anaconda3/envs/taxonomer/compiler_compat/ld: build/temp.linux-x86_64-2.7/src/query_db.o:/data/home/wlzhang/classfication/software/kraken2/taxonomer_0.5-0.5/taxonomer/src/load_dbs.h:41: multiple definition of `seqid_taxid_rel'; build/temp.linux-x86_64-2.7/scripts/cython/binner_PY.o:/data/home/wlzhang/classfication/software/kraken2/taxonomer_0.5-0.5/taxonomer/scripts/cython/../../src/load_dbs.h:41: first defined here
/data/home/wlzhang/anaconda3/envs/taxonomer/compiler_compat/ld: build/temp.linux-x86_64-2.7/src/kmer_utils.o:/data/home/wlzhang/classfication/software/kraken2/taxonomer_0.5-0.5/taxonomer/src/kmer_utils.h:32: multiple definition of `tax_globals'; build/temp.linux-x86_64-2.7/scripts/cython/binner_PY.o:/data/home/wlzhang/classfication/software/kraken2/taxonomer_0.5-0.5/taxonomer/scripts/cython/../../src/kmer_utils.h:32: first defined here
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1

@zhang570221322 zhang570221322 changed the title Biopython requires Python 3.6 or later. Python 2.7 detected. collect2: error: ld returned 1 exit status error: command 'gcc' failed with exit status Apr 12, 2022
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