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jbloomlab / dms_variants

Analyze deep mutational scanning of barcoded variants.
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Errors while installing dms_variants 1.1.0 with python 3.8 #73

Closed yeli7068 closed 2 years ago

yeli7068 commented 2 years ago

Dear Colleague,

Thanks for introducing this wonderful tool. I am tring to install dms_variants through instructions.

conda creat -n EscapeScore python=3.8 pip install dms_variants

It returned errors as: 

ERROR: Command errored out with exit status 1:
   command: /home/visitor3/miniconda3/envs/EscapeScore/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-x6sebrcu/dms-variants_d364475268bf4342bcc93bf4081bd52a/setup.py'"'"'; __file__='"'"'/tmp/pip-install-x6sebrcu/dms-variants_d364475268bf4342bcc93bf4081bd52a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-kjcst3n4
       cwd: /tmp/pip-install-x6sebrcu/dms-variants_d364475268bf4342bcc93bf4081bd52a/
  Complete output (160 lines):
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.linux-x86_64-3.8
  creating build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/__init__.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/barcodes.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/bottlenecks.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/codonvarianttable.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/constants.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/fastq.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/globalepistasis.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/illuminabarcodeparser.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/ispline.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/pdb_utils.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/plotnine_themes.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/simulate.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/utils.py -> build/lib.linux-x86_64-3.8/dms_variants
  running build_ext
  building 'dms_variants._cutils' extension
  creating build/temp.linux-x86_64-3.8
  creating build/temp.linux-x86_64-3.8/dms_variants
  gcc -pthread -B /home/visitor3/miniconda3/envs/EscapeScore/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/visitor3/miniconda3/envs/EscapeScore/include/python3.8 -c dms_variants/_cutils.c -o build/temp.linux-x86_64-3.8/dms_variants/_cutils.o -Wno-error=declaration-after-statement
  /tmp/ccFlUHig.s: Assembler messages:
  /tmp/ccFlUHig.s:18: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:18: Error: junk at end of line, first unrecognized character is `-'
  /tmp/ccFlUHig.s:20: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:20: Error: unknown pseudo-op: `.lvu1'
  /tmp/ccFlUHig.s:21: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:21: Error: unknown pseudo-op: `.lvu2'
  /tmp/ccFlUHig.s:22: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:22: Error: unknown pseudo-op: `.lvu3'
  /tmp/ccFlUHig.s:23: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:23: Error: unknown pseudo-op: `.lvu4'
  /tmp/ccFlUHig.s:24: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:24: Error: unknown pseudo-op: `.lvu5'
  /tmp/ccFlUHig.s:30: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:30: Error: unknown pseudo-op: `.lvu6'
  /tmp/ccFlUHig.s:34: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:34: Error: unknown pseudo-op: `.lvu7'
  /tmp/ccFlUHig.s:38: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:38: Error: unknown pseudo-op: `.lvu8'
  /tmp/ccFlUHig.s:40: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:40: Error: unknown pseudo-op: `.lvu9'
  /tmp/ccFlUHig.s:46: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:46: Error: unknown pseudo-op: `.lvu10'
  /tmp/ccFlUHig.s:50: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:50: Error: unknown pseudo-op: `.lvu11'
  /tmp/ccFlUHig.s:53: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:53: Error: unknown pseudo-op: `.lvu12'
  /tmp/ccFlUHig.s:54: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:54: Error: unknown pseudo-op: `.lvu13'
  /tmp/ccFlUHig.s:58: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:58: Error: unknown pseudo-op: `.lvu14'
  /tmp/ccFlUHig.s:60: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:60: Error: unknown pseudo-op: `.lvu15'
  /tmp/ccFlUHig.s:63: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:63: Error: unknown pseudo-op: `.lvu16'
  /tmp/ccFlUHig.s:64: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:64: Error: unknown pseudo-op: `.lvu17'
  /tmp/ccFlUHig.s:67: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:67: Error: unknown pseudo-op: `.lvu18'
  /tmp/ccFlUHig.s:70: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:70: Error: unknown pseudo-op: `.lvu19'
  /tmp/ccFlUHig.s:71: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:71: Error: unknown pseudo-op: `.lvu20'
  /tmp/ccFlUHig.s:74: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:74: Error: unknown pseudo-op: `.lvu21'
  /tmp/ccFlUHig.s:75: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:75: Error: unknown pseudo-op: `.lvu22'
  /tmp/ccFlUHig.s:77: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:77: Error: unknown pseudo-op: `.lvu23'
  /tmp/ccFlUHig.s:79: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:79: Error: unknown pseudo-op: `.lvu24'
  /tmp/ccFlUHig.s:80: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:80: Error: unknown pseudo-op: `.lvu25'
  /tmp/ccFlUHig.s:89: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:89: Error: unknown pseudo-op: `.lvu26'
  /tmp/ccFlUHig.s:90: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:90: Error: unknown pseudo-op: `.lvu27'
  /tmp/ccFlUHig.s:130: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:130: Error: unknown pseudo-op: `.lvu28'
  /tmp/ccFlUHig.s:131: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:131: Error: unknown pseudo-op: `.lvu29'
  /tmp/ccFlUHig.s:133: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:133: Error: unknown pseudo-op: `.lvu30'
  /tmp/ccFlUHig.s:135: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:135: Error: unknown pseudo-op: `.lvu31'
  /tmp/ccFlUHig.s:137: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:137: Error: unknown pseudo-op: `.lvu32'
  /tmp/ccFlUHig.s:140: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:140: Error: unknown pseudo-op: `.lvu33'
  /tmp/ccFlUHig.s:145: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:145: Error: unknown pseudo-op: `.lvu34'
  /tmp/ccFlUHig.s:146: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:146: Error: unknown pseudo-op: `.lvu35'
  /tmp/ccFlUHig.s:150: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:150: Error: unknown pseudo-op: `.lvu36'
  /tmp/ccFlUHig.s:152: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:152: Error: unknown pseudo-op: `.lvu37'
  /tmp/ccFlUHig.s:155: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:155: Error: unknown pseudo-op: `.lvu38'
  /tmp/ccFlUHig.s:158: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:158: Error: unknown pseudo-op: `.lvu39'
  /tmp/ccFlUHig.s:160: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:160: Error: unknown pseudo-op: `.lvu40'
  /tmp/ccFlUHig.s:177: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:177: Error: unknown pseudo-op: `.lvu41'
  /tmp/ccFlUHig.s:180: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:180: Error: unknown pseudo-op: `.lvu42'
  /tmp/ccFlUHig.s:182: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:182: Error: unknown pseudo-op: `.lvu43'
  /tmp/ccFlUHig.s:186: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:186: Error: unknown pseudo-op: `.lvu44'
  /tmp/ccFlUHig.s:187: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:187: Error: unknown pseudo-op: `.lvu45'
  /tmp/ccFlUHig.s:195: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:195: Error: unknown pseudo-op: `.lvu46'
  /tmp/ccFlUHig.s:199: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:199: Error: unknown pseudo-op: `.lvu47'
  /tmp/ccFlUHig.s:208: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:208: Error: unknown pseudo-op: `.lvu48'
  /tmp/ccFlUHig.s:209: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:209: Error: unknown pseudo-op: `.lvu49'
  /tmp/ccFlUHig.s:211: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:211: Error: unknown pseudo-op: `.lvu50'
  /tmp/ccFlUHig.s:216: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:216: Error: unknown pseudo-op: `.lvu51'
  /tmp/ccFlUHig.s:217: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:217: Error: unknown pseudo-op: `.lvu52'
  /tmp/ccFlUHig.s:219: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:219: Error: unknown pseudo-op: `.lvu53'
  /tmp/ccFlUHig.s:224: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:224: Error: unknown pseudo-op: `.lvu54'
  /tmp/ccFlUHig.s:225: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:225: Error: unknown pseudo-op: `.lvu55'
  /tmp/ccFlUHig.s:227: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:227: Error: unknown pseudo-op: `.lvu56'
  /tmp/ccFlUHig.s:232: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:232: Error: unknown pseudo-op: `.lvu57'
  /tmp/ccFlUHig.s:233: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:233: Error: unknown pseudo-op: `.lvu58'
  /tmp/ccFlUHig.s:235: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:235: Error: unknown pseudo-op: `.lvu59'
  /tmp/ccFlUHig.s:239: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:239: Error: unknown pseudo-op: `.lvu60'
  /tmp/ccFlUHig.s:242: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:242: Error: unknown pseudo-op: `.lvu61'
  /tmp/ccFlUHig.s:247: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:247: Error: unknown pseudo-op: `.lvu62'
  /tmp/ccFlUHig.s:248: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:248: Error: unknown pseudo-op: `.lvu63'
  /tmp/ccFlUHig.s:258: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:258: Error: junk at end of line, first unrecognized character is `-'
  /tmp/ccFlUHig.s:260: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:260: Error: unknown pseudo-op: `.lvu65'
  /tmp/ccFlUHig.s:261: Error: unknown .loc sub-directive `view'
  /tmp/ccFlUHig.s:261: Error: unknown pseudo-op: `.lvu66'
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for dms-variants
  Running setup.py clean for dms-variants
Failed to build dms-variants
Installing collected packages: dms-variants
    Running setup.py install for dms-variants ... error
    ERROR: Command errored out with exit status 1:
     command: /home/visitor3/miniconda3/envs/EscapeScore/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-x6sebrcu/dms-variants_d364475268bf4342bcc93bf4081bd52a/setup.py'"'"'; __file__='"'"'/tmp/pip-install-x6sebrcu/dms-variants_d364475268bf4342bcc93bf4081bd52a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ebqaddow/install-record.txt --single-version-externally-managed --compile --install-headers /home/visitor3/miniconda3/envs/EscapeScore/include/python3.8/dms-variants
         cwd: /tmp/pip-install-x6sebrcu/dms-variants_d364475268bf4342bcc93bf4081bd52a/
    Complete output (160 lines):
    running install
    running build
    running build_py
    creating build
    creating build/lib.linux-x86_64-3.8
    creating build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/__init__.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/barcodes.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/bottlenecks.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/codonvarianttable.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/constants.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/fastq.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/globalepistasis.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/illuminabarcodeparser.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/ispline.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/pdb_utils.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/plotnine_themes.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/simulate.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/utils.py -> build/lib.linux-x86_64-3.8/dms_variants
    running build_ext
    building 'dms_variants._cutils' extension
    creating build/temp.linux-x86_64-3.8
    creating build/temp.linux-x86_64-3.8/dms_variants
    gcc -pthread -B /home/visitor3/miniconda3/envs/EscapeScore/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/visitor3/miniconda3/envs/EscapeScore/include/python3.8 -c dms_variants/_cutils.c -o build/temp.linux-x86_64-3.8/dms_variants/_cutils.o -Wno-error=declaration-after-statement
    /tmp/cc3yijyQ.s: Assembler messages:
    /tmp/cc3yijyQ.s:18: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:18: Error: junk at end of line, first unrecognized character is `-'
    /tmp/cc3yijyQ.s:20: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:20: Error: unknown pseudo-op: `.lvu1'
    /tmp/cc3yijyQ.s:21: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:21: Error: unknown pseudo-op: `.lvu2'
    /tmp/cc3yijyQ.s:22: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:22: Error: unknown pseudo-op: `.lvu3'
    /tmp/cc3yijyQ.s:23: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:23: Error: unknown pseudo-op: `.lvu4'
    /tmp/cc3yijyQ.s:24: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:24: Error: unknown pseudo-op: `.lvu5'
    /tmp/cc3yijyQ.s:30: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:30: Error: unknown pseudo-op: `.lvu6'
    /tmp/cc3yijyQ.s:34: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:34: Error: unknown pseudo-op: `.lvu7'
    /tmp/cc3yijyQ.s:38: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:38: Error: unknown pseudo-op: `.lvu8'
    /tmp/cc3yijyQ.s:40: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:40: Error: unknown pseudo-op: `.lvu9'
    /tmp/cc3yijyQ.s:46: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:46: Error: unknown pseudo-op: `.lvu10'
    /tmp/cc3yijyQ.s:50: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:50: Error: unknown pseudo-op: `.lvu11'
    /tmp/cc3yijyQ.s:53: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:53: Error: unknown pseudo-op: `.lvu12'
    /tmp/cc3yijyQ.s:54: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:54: Error: unknown pseudo-op: `.lvu13'
    /tmp/cc3yijyQ.s:58: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:58: Error: unknown pseudo-op: `.lvu14'
    /tmp/cc3yijyQ.s:60: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:60: Error: unknown pseudo-op: `.lvu15'
    /tmp/cc3yijyQ.s:63: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:63: Error: unknown pseudo-op: `.lvu16'
    /tmp/cc3yijyQ.s:64: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:64: Error: unknown pseudo-op: `.lvu17'
    /tmp/cc3yijyQ.s:67: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:67: Error: unknown pseudo-op: `.lvu18'
    /tmp/cc3yijyQ.s:70: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:70: Error: unknown pseudo-op: `.lvu19'
    /tmp/cc3yijyQ.s:71: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:71: Error: unknown pseudo-op: `.lvu20'
    /tmp/cc3yijyQ.s:74: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:74: Error: unknown pseudo-op: `.lvu21'
    /tmp/cc3yijyQ.s:75: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:75: Error: unknown pseudo-op: `.lvu22'
    /tmp/cc3yijyQ.s:77: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:77: Error: unknown pseudo-op: `.lvu23'
    /tmp/cc3yijyQ.s:79: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:79: Error: unknown pseudo-op: `.lvu24'
    /tmp/cc3yijyQ.s:80: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:80: Error: unknown pseudo-op: `.lvu25'
    /tmp/cc3yijyQ.s:89: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:89: Error: unknown pseudo-op: `.lvu26'
    /tmp/cc3yijyQ.s:90: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:90: Error: unknown pseudo-op: `.lvu27'
    /tmp/cc3yijyQ.s:130: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:130: Error: unknown pseudo-op: `.lvu28'
    /tmp/cc3yijyQ.s:131: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:131: Error: unknown pseudo-op: `.lvu29'
    /tmp/cc3yijyQ.s:133: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:133: Error: unknown pseudo-op: `.lvu30'
    /tmp/cc3yijyQ.s:135: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:135: Error: unknown pseudo-op: `.lvu31'
    /tmp/cc3yijyQ.s:137: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:137: Error: unknown pseudo-op: `.lvu32'
    /tmp/cc3yijyQ.s:140: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:140: Error: unknown pseudo-op: `.lvu33'
    /tmp/cc3yijyQ.s:145: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:145: Error: unknown pseudo-op: `.lvu34'
    /tmp/cc3yijyQ.s:146: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:146: Error: unknown pseudo-op: `.lvu35'
    /tmp/cc3yijyQ.s:150: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:150: Error: unknown pseudo-op: `.lvu36'
    /tmp/cc3yijyQ.s:152: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:152: Error: unknown pseudo-op: `.lvu37'
    /tmp/cc3yijyQ.s:155: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:155: Error: unknown pseudo-op: `.lvu38'
    /tmp/cc3yijyQ.s:158: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:158: Error: unknown pseudo-op: `.lvu39'
    /tmp/cc3yijyQ.s:160: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:160: Error: unknown pseudo-op: `.lvu40'
    /tmp/cc3yijyQ.s:177: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:177: Error: unknown pseudo-op: `.lvu41'
    /tmp/cc3yijyQ.s:180: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:180: Error: unknown pseudo-op: `.lvu42'
    /tmp/cc3yijyQ.s:182: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:182: Error: unknown pseudo-op: `.lvu43'
    /tmp/cc3yijyQ.s:186: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:186: Error: unknown pseudo-op: `.lvu44'
    /tmp/cc3yijyQ.s:187: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:187: Error: unknown pseudo-op: `.lvu45'
    /tmp/cc3yijyQ.s:195: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:195: Error: unknown pseudo-op: `.lvu46'
    /tmp/cc3yijyQ.s:199: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:199: Error: unknown pseudo-op: `.lvu47'
    /tmp/cc3yijyQ.s:208: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:208: Error: unknown pseudo-op: `.lvu48'
    /tmp/cc3yijyQ.s:209: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:209: Error: unknown pseudo-op: `.lvu49'
    /tmp/cc3yijyQ.s:211: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:211: Error: unknown pseudo-op: `.lvu50'
    /tmp/cc3yijyQ.s:216: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:216: Error: unknown pseudo-op: `.lvu51'
    /tmp/cc3yijyQ.s:217: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:217: Error: unknown pseudo-op: `.lvu52'
    /tmp/cc3yijyQ.s:219: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:219: Error: unknown pseudo-op: `.lvu53'
    /tmp/cc3yijyQ.s:224: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:224: Error: unknown pseudo-op: `.lvu54'
    /tmp/cc3yijyQ.s:225: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:225: Error: unknown pseudo-op: `.lvu55'
    /tmp/cc3yijyQ.s:227: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:227: Error: unknown pseudo-op: `.lvu56'
    /tmp/cc3yijyQ.s:232: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:232: Error: unknown pseudo-op: `.lvu57'
    /tmp/cc3yijyQ.s:233: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:233: Error: unknown pseudo-op: `.lvu58'
    /tmp/cc3yijyQ.s:235: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:235: Error: unknown pseudo-op: `.lvu59'
    /tmp/cc3yijyQ.s:239: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:239: Error: unknown pseudo-op: `.lvu60'
    /tmp/cc3yijyQ.s:242: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:242: Error: unknown pseudo-op: `.lvu61'
    /tmp/cc3yijyQ.s:247: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:247: Error: unknown pseudo-op: `.lvu62'
    /tmp/cc3yijyQ.s:248: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:248: Error: unknown pseudo-op: `.lvu63'
    /tmp/cc3yijyQ.s:258: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:258: Error: junk at end of line, first unrecognized character is `-'
    /tmp/cc3yijyQ.s:260: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:260: Error: unknown pseudo-op: `.lvu65'
    /tmp/cc3yijyQ.s:261: Error: unknown .loc sub-directive `view'
    /tmp/cc3yijyQ.s:261: Error: unknown pseudo-op: `.lvu66'
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/visitor3/miniconda3/envs/EscapeScore/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-x6sebrcu/dms-variants_d364475268bf4342bcc93bf4081bd52a/setup.py'"'"'; __file__='"'"'/tmp/pip-install-x6sebrcu/dms-variants_d364475268bf4342bcc93bf4081bd52a/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-ebqaddow/install-record.txt --single-version-externally-managed --compile --install-headers /home/visitor3/miniconda3/envs/EscapeScore/include/python3.8/dms-variants Check the logs for full command output.

The system info:

gcc version 9.3.0 (GCC) CentOS Linux release 7.7.1908 (Core) Python 3.8.12

Thanks in advance!

Young

jbloom commented 2 years ago

Hmmm, we don't get this error. I'm not sure the cause, but I suspect it has something to do with the gcc libraries on your particular computer and if so that is going to be over my head to troubleshoot. It seems to be some problem in the assembly language and not in the dms_variants code itself.

Can you try building a different conda environment with say a different installation of gcc or python? (Probably gcc.)

yeli7068 commented 2 years ago

Thanks for the quick response, Dr. Bloom. I just ran a quick test on my PC, it worked. I am going to install the other version of gcc on the sever with conda. Thanks again!

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发件人: Jesse Bloom @.> 发送时间: Thursday, December 16, 2021 11:27:44 PM 收件人: jbloomlab/dms_variants @.> 抄送: yeli7068 @.>; Author @.> 主题: Re: [jbloomlab/dms_variants] Errors while installing dms_variants 1.1.0 with python 3.8 (Issue #73)

Hmmm, we don't get this error. I'm not sure the cause, but I suspect it has something to do with the gcc libraries on your particular computer and if so that is going to be over my head to troubleshoot. It seems to be some problem in the assembly language and not in the dms_variants code itself.

Can you try building a different conda environment with say a different installation of gcc or python?

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yeli7068 commented 2 years ago

This issue has been fixed through installing a new gcc under the conda environment.

conda install -c conda-forge gcc
pip install dms_variants