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jbloomlab / dms_variants

Analyze deep mutational scanning of barcoded variants.
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pip install issue #72

Closed Bernadetadad closed 2 years ago

Bernadetadad commented 2 years ago

I'm running env create -f environment.txt to create environment that has dms_variants in it and I get this error:

Pip subprocess error:
  ERROR: Command errored out with exit status 1:
   command: /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nb8htshi/dms-variants_ed4b7e3400d646d6b252d2e15d530538/setup.py'"'"'; __file__='"'"'/tmp/pip-install-nb8htshi/dms-variants_ed4b7e3400d646d6b252d2e15d530538/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-ef91g30z
       cwd: /tmp/pip-install-nb8htshi/dms-variants_ed4b7e3400d646d6b252d2e15d530538/
  Complete output (30 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/simulate.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/bottlenecks.py -> 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/pdb_utils.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/binarymap.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/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/barcodes.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/constants.py -> build/lib.linux-x86_64-3.8/dms_variants
  copying dms_variants/ispline.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/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/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
  gcc -pthread -shared -B /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/compiler_compat -L/home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/lib -Wl,-rpath=/home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/bdadonai/miniconda3/lib -Wl,-rpath-link,/home/bdadonai/miniconda3/lib -L/home/bdadonai/miniconda3/lib build/temp.linux-x86_64-3.8/dms_variants/_cutils.o -o build/lib.linux-x86_64-3.8/dms_variants/_cutils.cpython-38-x86_64-linux-gnu.so
  /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/compiler_compat/ld: cannot find /lib/libpthread.so.0
  /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/compiler_compat/ld: cannot find /usr/lib/libpthread_nonshared.a
  collect2: error: ld returned 1 exit status
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for dms-variants
    ERROR: Command errored out with exit status 1:
     command: /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nb8htshi/dms-variants_ed4b7e3400d646d6b252d2e15d530538/setup.py'"'"'; __file__='"'"'/tmp/pip-install-nb8htshi/dms-variants_ed4b7e3400d646d6b252d2e15d530538/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-d13blf8b/install-record.txt --single-version-externally-managed --compile --install-headers /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/include/python3.8/dms-variants
         cwd: /tmp/pip-install-nb8htshi/dms-variants_ed4b7e3400d646d6b252d2e15d530538/
    Complete output (32 lines):
    running install
    /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/lib/python3.8/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
      warnings.warn(
    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/simulate.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/bottlenecks.py -> 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/pdb_utils.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/binarymap.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/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/barcodes.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/constants.py -> build/lib.linux-x86_64-3.8/dms_variants
    copying dms_variants/ispline.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/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/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
    gcc -pthread -shared -B /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/compiler_compat -L/home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/lib -Wl,-rpath=/home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/lib -Wl,--no-as-needed -Wl,--sysroot=/ -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/bdadonai/miniconda3/lib -Wl,-rpath-link,/home/bdadonai/miniconda3/lib -L/home/bdadonai/miniconda3/lib build/temp.linux-x86_64-3.8/dms_variants/_cutils.o -o build/lib.linux-x86_64-3.8/dms_variants/_cutils.cpython-38-x86_64-linux-gnu.so
    /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/compiler_compat/ld: cannot find /lib/libpthread.so.0
    /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/compiler_compat/ld: cannot find /usr/lib/libpthread_nonshared.a
    collect2: error: ld returned 1 exit status
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-nb8htshi/dms-variants_ed4b7e3400d646d6b252d2e15d530538/setup.py'"'"'; __file__='"'"'/tmp/pip-install-nb8htshi/dms-variants_ed4b7e3400d646d6b252d2e15d530538/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-d13blf8b/install-record.txt --single-version-externally-managed --compile --install-headers /home/bdadonai/miniconda3/envs/SARS-CoV-2_Delta_spike_DMS/include/python3.8/dms-variants Check the logs for full command output.

failed

CondaEnvException: Pip failed

If I run env create -f environment_1.txt that only has pip and dms_variants in it it works fine.

environment_1.txt environment.txt

jbloom commented 2 years ago

Can you sequentially add back the other packages in environment.txt to environment_1.txt and figure out which one is causing the problem?

Bernadetadad commented 2 years ago

I'm going to close this issue. Don't know why but I could not get any of this working from the Hutch, but now on VPN from home all works totally fine.