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ERROR: Failed building wheel for biskit

Open manu123416 opened this issue 3 years ago • 1 comments

Hello Sir, I tried installing Biskit as below and am getting the Error:

(base) m992c693@alveo:~$ pip install biskit
Collecting biskit
  Downloading biskit-2.4.3.tar.gz (20.5 MB)
     |████████████████████████████████| 20.5 MB 20.2 MB/s
Requirement already satisfied: numpy in ./anaconda3/lib/python3.9/site-packages (from biskit) (1.21.5)
Requirement already satisfied: scipy in ./anaconda3/lib/python3.9/site-packages (from biskit) (1.7.3)
Collecting biopython
  Downloading biopython-1.79-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.7 MB)
     |████████████████████████████████| 2.7 MB 63.3 MB/s
Building wheels for collected packages: biskit
  Building wheel for biskit (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/m992c693/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"'; __file__='"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/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-w6oip1d1
       cwd: /tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/
  Complete output (190 lines):
  /home/m992c693/anaconda3/lib/python3.9/site-packages/setuptools/dist.py:757: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
    warnings.warn(
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib
  creating build/lib/Biskit
  copying Biskit/molUtils.py -> build/lib/Biskit
  copying Biskit/ExeConfig.py -> build/lib/Biskit
  copying Biskit/ExeConfigCache.py -> build/lib/Biskit
  copying Biskit/PCRModel.py -> build/lib/Biskit
  copying Biskit/Model.py -> build/lib/Biskit
  copying Biskit/Trajectory.py -> build/lib/Biskit
  copying Biskit/SettingsParser.py -> build/lib/Biskit
  copying Biskit/molTools.py -> build/lib/Biskit
  copying Biskit/DSSP.py -> build/lib/Biskit
  copying Biskit/AmberRstParser.py -> build/lib/Biskit
  copying Biskit/BioUnit.py -> build/lib/Biskit
  copying Biskit/PDBParserFactory.py -> build/lib/Biskit
  copying Biskit/PDBParseNCBI.py -> build/lib/Biskit
  copying Biskit/Executor.py -> build/lib/Biskit
  copying Biskit/wormlikechain.py -> build/lib/Biskit
  copying Biskit/SurfaceRacer.py -> build/lib/Biskit
  copying Biskit/amberResidues.py -> build/lib/Biskit
  copying Biskit/QualSlave.py -> build/lib/Biskit
  copying Biskit/CommandLine.py -> build/lib/Biskit
  copying Biskit/PDBModel.py -> build/lib/Biskit
  copying Biskit/AmberParmBuilder.py -> build/lib/Biskit
  copying Biskit/ModelList.py -> build/lib/Biskit
  copying Biskit/Hmmer.py -> build/lib/Biskit
  copying Biskit/gnuplot.py -> build/lib/Biskit
  copying Biskit/ProfileMirror.py -> build/lib/Biskit
  copying Biskit/LocalPath.py -> build/lib/Biskit
  copying Biskit/reduce.py -> build/lib/Biskit
  copying Biskit/TrajFlexMaster.py -> build/lib/Biskit
  copying Biskit/PDBParseModel.py -> build/lib/Biskit
  copying Biskit/AmberCrdParser.py -> build/lib/Biskit
  copying Biskit/ErrorHandler.py -> build/lib/Biskit
  copying Biskit/decorators.py -> build/lib/Biskit
  copying Biskit/AmberCrdEntropist.py -> build/lib/Biskit
  copying Biskit/PDBParsePickle.py -> build/lib/Biskit
  copying Biskit/amberResidueLibrary.py -> build/lib/Biskit
  copying Biskit/Polymer.py -> build/lib/Biskit
  copying Biskit/StructureMaster.py -> build/lib/Biskit
  copying Biskit/surfaceRacerTools.py -> build/lib/Biskit
  copying Biskit/ReduceCoordinates.py -> build/lib/Biskit
  copying Biskit/ColorSpectrum.py -> build/lib/Biskit
  copying Biskit/FuzzyCluster.py -> build/lib/Biskit
  copying Biskit/PDBCleaner.py -> build/lib/Biskit
  copying Biskit/Xplorer.py -> build/lib/Biskit
  copying Biskit/PDBDope.py -> build/lib/Biskit
  copying Biskit/WhatIf.py -> build/lib/Biskit
  copying Biskit/AmberEntropist.py -> build/lib/Biskit
  copying Biskit/ProfileCollection.py -> build/lib/Biskit
  copying Biskit/AmberEntropySlave.py -> build/lib/Biskit
  copying Biskit/Blast2Seq.py -> build/lib/Biskit
  copying Biskit/match2seq.py -> build/lib/Biskit
  copying Biskit/mathUtils.py -> build/lib/Biskit
  copying Biskit/DictList.py -> build/lib/Biskit
  copying Biskit/wlc.py -> build/lib/Biskit
  copying Biskit/residue.py -> build/lib/Biskit
  copying Biskit/TrajFlexSlave.py -> build/lib/Biskit
  copying Biskit/MatrixPlot.py -> build/lib/Biskit
  copying Biskit/ez_setup.py -> build/lib/Biskit
  copying Biskit/Fold_X.py -> build/lib/Biskit
  copying Biskit/QualMaster.py -> build/lib/Biskit
  copying Biskit/hist.py -> build/lib/Biskit
  copying Biskit/atomCharger.py -> build/lib/Biskit
  copying Biskit/SparseArray.py -> build/lib/Biskit
  copying Biskit/difflib_old.py -> build/lib/Biskit
  copying Biskit/tmalign.py -> build/lib/Biskit
  copying Biskit/EnsembleTraj.py -> build/lib/Biskit
  copying Biskit/test.py -> build/lib/Biskit
  copying Biskit/__init__.py -> build/lib/Biskit
  copying Biskit/EDParser.py -> build/lib/Biskit
  copying Biskit/Prosa2003.py -> build/lib/Biskit
  copying Biskit/PDBParseFile.py -> build/lib/Biskit
  copying Biskit/SettingsManager.py -> build/lib/Biskit
  copying Biskit/Pymoler.py -> build/lib/Biskit
  copying Biskit/tools.py -> build/lib/Biskit
  copying Biskit/msms.py -> build/lib/Biskit
  copying Biskit/Errors.py -> build/lib/Biskit
  copying Biskit/LogFile.py -> build/lib/Biskit
  copying Biskit/settings.py -> build/lib/Biskit
  copying Biskit/BisList.py -> build/lib/Biskit
  copying Biskit/plotUtils.py -> build/lib/Biskit
  copying Biskit/Ramachandran.py -> build/lib/Biskit
  copying Biskit/AmberLeap.py -> build/lib/Biskit
  copying Biskit/TrajCluster.py -> build/lib/Biskit
  copying Biskit/AmberEntropyMaster.py -> build/lib/Biskit
  copying Biskit/IcmCad.py -> build/lib/Biskit
  copying Biskit/rmsFit.py -> build/lib/Biskit
  copying Biskit/XplorInput.py -> build/lib/Biskit
  copying Biskit/PDBParser.py -> build/lib/Biskit
  copying Biskit/delphi.py -> build/lib/Biskit
  copying Biskit/StructureSlave.py -> build/lib/Biskit
  creating build/lib/Biskit/Mod
  copying Biskit/Mod/Analyse.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/ModelSlave.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/Modeller.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/TemplateSearcher.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/TemplateFilter.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/ModelMaster.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/AlignerMaster.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/ValidationSetup.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/TemplateCleaner.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/Benchmark.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/modUtils.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/__init__.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/Aligner.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/AlignerSlave.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/SequenceSearcher.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/settings.py -> build/lib/Biskit/Mod
  copying Biskit/Mod/CheckIdentities.py -> build/lib/Biskit/Mod
  creating build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/PDBExportFilters.py -> build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/PDB.py -> build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/__init__.py -> build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/FortranFormat.py -> build/lib/Biskit/ScientificIO
  copying Biskit/ScientificIO/TextFile.py -> build/lib/Biskit/ScientificIO
  creating build/lib/Biskit/deprecated
  copying Biskit/deprecated/ChainWriter.py -> build/lib/Biskit/deprecated
  copying Biskit/deprecated/__init__.py -> build/lib/Biskit/deprecated
  copying Biskit/deprecated/ChainSeparator.py -> build/lib/Biskit/deprecated
  copying Biskit/deprecated/ChainCleaner.py -> build/lib/Biskit/deprecated
  creating build/lib/Biskit/Statistics
  copying Biskit/Statistics/Density.py -> build/lib/Biskit/Statistics
  copying Biskit/Statistics/ROCalyzer.py -> build/lib/Biskit/Statistics
  copying Biskit/Statistics/__init__.py -> build/lib/Biskit/Statistics
  copying Biskit/Statistics/lognormal.py -> build/lib/Biskit/Statistics
  creating build/lib/Biskit/PVM
  copying Biskit/PVM/Status.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/dispatcher.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/TrackingJobMaster.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/pvm.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/hosts.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/ExampleSlave.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/PVMThread.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/__init__.py -> build/lib/Biskit/PVM
  copying Biskit/PVM/ExampleMaster.py -> build/lib/Biskit/PVM
  creating build/lib/Biskit/Dock
  copying Biskit/Dock/XRefineComplex.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexEvolving.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/Analyzer.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexRandomizer.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexList.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ContactSlave.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexModelRegistry.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexEvolvingList.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ComplexTraj.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/PatchGeneratorFromOrbit.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/HexParser.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/PatchGenerator.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/Intervor.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/hexTools.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/__init__.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/delphiBindingEnergy.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/settings.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/Complex.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/FixedList.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/Docker.py -> build/lib/Biskit/Dock
  copying Biskit/Dock/ContactMaster.py -> build/lib/Biskit/Dock
  creating build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/ufuncs.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/compat.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/typeconv.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/alter_code.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/__init__.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/functions.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/array_printer.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/misc.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/precision.py -> build/lib/Biskit/oldnumeric
  copying Biskit/oldnumeric/__analyze_oldnumeric.py -> build/lib/Biskit/oldnumeric
  running egg_info
  writing biskit.egg-info/PKG-INFO
  writing dependency_links to biskit.egg-info/dependency_links.txt
  writing requirements to biskit.egg-info/requires.txt
  writing top-level names to biskit.egg-info/top_level.txt
  reading manifest file 'biskit.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE.txt'
  writing manifest file 'biskit.egg-info/SOURCES.txt'
  error: Error: setup script specifies an absolute path:
 
      /tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/Biskit/data/[spectrum.pl](http://spectrum.pl/)
 
  setup() arguments must *always* be /-separated paths relative to the
  setup.py directory, *never* absolute paths.
 
  ----------------------------------------
  ERROR: Failed building wheel for biskit
  Running setup.py clean for biskit
Failed to build biskit
Installing collected packages: biopython, biskit
    Running setup.py install for biskit ... error
    ERROR: Command errored out with exit status 1:
     command: /home/m992c693/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"'; __file__='"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/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-kgonm3c0/install-record.txt --single-version-externally-managed --compile --install-headers /home/m992c693/anaconda3/include/python3.9/biskit
         cwd: /tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/
    Complete output (192 lines):
    /home/m992c693/anaconda3/lib/python3.9/site-packages/setuptools/dist.py:757: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
      warnings.warn(
    running install
    /home/m992c693/anaconda3/lib/python3.9/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
    creating build/lib/Biskit
    copying Biskit/molUtils.py -> build/lib/Biskit
    copying Biskit/ExeConfig.py -> build/lib/Biskit
    copying Biskit/ExeConfigCache.py -> build/lib/Biskit
    copying Biskit/PCRModel.py -> build/lib/Biskit
    copying Biskit/Model.py -> build/lib/Biskit
    copying Biskit/Trajectory.py -> build/lib/Biskit
    copying Biskit/SettingsParser.py -> build/lib/Biskit
    copying Biskit/molTools.py -> build/lib/Biskit
    copying Biskit/DSSP.py -> build/lib/Biskit
    copying Biskit/AmberRstParser.py -> build/lib/Biskit
    copying Biskit/BioUnit.py -> build/lib/Biskit
    copying Biskit/PDBParserFactory.py -> build/lib/Biskit
    copying Biskit/PDBParseNCBI.py -> build/lib/Biskit
    copying Biskit/Executor.py -> build/lib/Biskit
    copying Biskit/wormlikechain.py -> build/lib/Biskit
    copying Biskit/SurfaceRacer.py -> build/lib/Biskit
    copying Biskit/amberResidues.py -> build/lib/Biskit
    copying Biskit/QualSlave.py -> build/lib/Biskit
    copying Biskit/CommandLine.py -> build/lib/Biskit
    copying Biskit/PDBModel.py -> build/lib/Biskit
    copying Biskit/AmberParmBuilder.py -> build/lib/Biskit
    copying Biskit/ModelList.py -> build/lib/Biskit
    copying Biskit/Hmmer.py -> build/lib/Biskit
    copying Biskit/gnuplot.py -> build/lib/Biskit
    copying Biskit/ProfileMirror.py -> build/lib/Biskit
    copying Biskit/LocalPath.py -> build/lib/Biskit
    copying Biskit/reduce.py -> build/lib/Biskit
    copying Biskit/TrajFlexMaster.py -> build/lib/Biskit
    copying Biskit/PDBParseModel.py -> build/lib/Biskit
    copying Biskit/AmberCrdParser.py -> build/lib/Biskit
    copying Biskit/ErrorHandler.py -> build/lib/Biskit
    copying Biskit/decorators.py -> build/lib/Biskit
    copying Biskit/AmberCrdEntropist.py -> build/lib/Biskit
    copying Biskit/PDBParsePickle.py -> build/lib/Biskit
    copying Biskit/amberResidueLibrary.py -> build/lib/Biskit
    copying Biskit/Polymer.py -> build/lib/Biskit
    copying Biskit/StructureMaster.py -> build/lib/Biskit
    copying Biskit/surfaceRacerTools.py -> build/lib/Biskit
    copying Biskit/ReduceCoordinates.py -> build/lib/Biskit
    copying Biskit/ColorSpectrum.py -> build/lib/Biskit
    copying Biskit/FuzzyCluster.py -> build/lib/Biskit
    copying Biskit/PDBCleaner.py -> build/lib/Biskit
    copying Biskit/Xplorer.py -> build/lib/Biskit
    copying Biskit/PDBDope.py -> build/lib/Biskit
    copying Biskit/WhatIf.py -> build/lib/Biskit
    copying Biskit/AmberEntropist.py -> build/lib/Biskit
    copying Biskit/ProfileCollection.py -> build/lib/Biskit
    copying Biskit/AmberEntropySlave.py -> build/lib/Biskit
    copying Biskit/Blast2Seq.py -> build/lib/Biskit
    copying Biskit/match2seq.py -> build/lib/Biskit
    copying Biskit/mathUtils.py -> build/lib/Biskit
    copying Biskit/DictList.py -> build/lib/Biskit
    copying Biskit/wlc.py -> build/lib/Biskit
    copying Biskit/residue.py -> build/lib/Biskit
    copying Biskit/TrajFlexSlave.py -> build/lib/Biskit
    copying Biskit/MatrixPlot.py -> build/lib/Biskit
    copying Biskit/ez_setup.py -> build/lib/Biskit
    copying Biskit/Fold_X.py -> build/lib/Biskit
    copying Biskit/QualMaster.py -> build/lib/Biskit
    copying Biskit/hist.py -> build/lib/Biskit
    copying Biskit/atomCharger.py -> build/lib/Biskit
    copying Biskit/SparseArray.py -> build/lib/Biskit
    copying Biskit/difflib_old.py -> build/lib/Biskit
    copying Biskit/tmalign.py -> build/lib/Biskit
    copying Biskit/EnsembleTraj.py -> build/lib/Biskit
    copying Biskit/test.py -> build/lib/Biskit
    copying Biskit/__init__.py -> build/lib/Biskit
    copying Biskit/EDParser.py -> build/lib/Biskit
    copying Biskit/Prosa2003.py -> build/lib/Biskit
    copying Biskit/PDBParseFile.py -> build/lib/Biskit
    copying Biskit/SettingsManager.py -> build/lib/Biskit
    copying Biskit/Pymoler.py -> build/lib/Biskit
    copying Biskit/tools.py -> build/lib/Biskit
    copying Biskit/msms.py -> build/lib/Biskit
    copying Biskit/Errors.py -> build/lib/Biskit
    copying Biskit/LogFile.py -> build/lib/Biskit
    copying Biskit/settings.py -> build/lib/Biskit
    copying Biskit/BisList.py -> build/lib/Biskit
    copying Biskit/plotUtils.py -> build/lib/Biskit
    copying Biskit/Ramachandran.py -> build/lib/Biskit
    copying Biskit/AmberLeap.py -> build/lib/Biskit
    copying Biskit/TrajCluster.py -> build/lib/Biskit
    copying Biskit/AmberEntropyMaster.py -> build/lib/Biskit
    copying Biskit/IcmCad.py -> build/lib/Biskit
    copying Biskit/rmsFit.py -> build/lib/Biskit
    copying Biskit/XplorInput.py -> build/lib/Biskit
    copying Biskit/PDBParser.py -> build/lib/Biskit
    copying Biskit/delphi.py -> build/lib/Biskit
    copying Biskit/StructureSlave.py -> build/lib/Biskit
    creating build/lib/Biskit/Mod
    copying Biskit/Mod/Analyse.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/ModelSlave.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/Modeller.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/TemplateSearcher.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/TemplateFilter.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/ModelMaster.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/AlignerMaster.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/ValidationSetup.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/TemplateCleaner.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/Benchmark.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/modUtils.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/__init__.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/Aligner.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/AlignerSlave.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/SequenceSearcher.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/settings.py -> build/lib/Biskit/Mod
    copying Biskit/Mod/CheckIdentities.py -> build/lib/Biskit/Mod
    creating build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/PDBExportFilters.py -> build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/PDB.py -> build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/__init__.py -> build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/FortranFormat.py -> build/lib/Biskit/ScientificIO
    copying Biskit/ScientificIO/TextFile.py -> build/lib/Biskit/ScientificIO
    creating build/lib/Biskit/deprecated
    copying Biskit/deprecated/ChainWriter.py -> build/lib/Biskit/deprecated
    copying Biskit/deprecated/__init__.py -> build/lib/Biskit/deprecated
    copying Biskit/deprecated/ChainSeparator.py -> build/lib/Biskit/deprecated
    copying Biskit/deprecated/ChainCleaner.py -> build/lib/Biskit/deprecated
    creating build/lib/Biskit/Statistics
    copying Biskit/Statistics/Density.py -> build/lib/Biskit/Statistics
    copying Biskit/Statistics/ROCalyzer.py -> build/lib/Biskit/Statistics
    copying Biskit/Statistics/__init__.py -> build/lib/Biskit/Statistics
    copying Biskit/Statistics/lognormal.py -> build/lib/Biskit/Statistics
    creating build/lib/Biskit/PVM
    copying Biskit/PVM/Status.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/dispatcher.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/TrackingJobMaster.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/pvm.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/hosts.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/ExampleSlave.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/PVMThread.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/__init__.py -> build/lib/Biskit/PVM
    copying Biskit/PVM/ExampleMaster.py -> build/lib/Biskit/PVM
    creating build/lib/Biskit/Dock
    copying Biskit/Dock/XRefineComplex.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexEvolving.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/Analyzer.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexRandomizer.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexList.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ContactSlave.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexModelRegistry.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexEvolvingList.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ComplexTraj.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/PatchGeneratorFromOrbit.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/HexParser.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/PatchGenerator.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/Intervor.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/hexTools.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/__init__.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/delphiBindingEnergy.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/settings.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/Complex.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/FixedList.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/Docker.py -> build/lib/Biskit/Dock
    copying Biskit/Dock/ContactMaster.py -> build/lib/Biskit/Dock
    creating build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/ufuncs.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/compat.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/typeconv.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/alter_code.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/__init__.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/functions.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/array_printer.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/misc.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/precision.py -> build/lib/Biskit/oldnumeric
    copying Biskit/oldnumeric/__analyze_oldnumeric.py -> build/lib/Biskit/oldnumeric
    running egg_info
    writing biskit.egg-info/PKG-INFO
    writing dependency_links to biskit.egg-info/dependency_links.txt
    writing requirements to biskit.egg-info/requires.txt
    writing top-level names to biskit.egg-info/top_level.txt
    reading manifest file 'biskit.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    adding license file 'LICENSE.txt'
    writing manifest file 'biskit.egg-info/SOURCES.txt'
    error: Error: setup script specifies an absolute path:
   
        /tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/Biskit/data/[spectrum.pl](http://spectrum.pl/)
   
    setup() arguments must *always* be /-separated paths relative to the
    setup.py directory, *never* absolute paths.
   
    ----------------------------------------
ERROR: Command errored out with exit status 1: /home/m992c693/anaconda3/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/setup.py'"'"'; __file__='"'"'/tmp/pip-install-85nis4sp/biskit_6b98ccddb80648f6a036f26da0929da3/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-kgonm3c0/install-record.txt --single-version-externally-managed --compile --install-headers /home/m992c693/anaconda3/include/python3.9/biskit Check the logs for full command output.

Not sure how to resolve this error and install biskit correctly. Thank you for the kind help.

manu123416 avatar Nov 10 '22 02:11 manu123416

Oh, haven't seen this one. I plan to look over the biskit code base over the next two months. A big layer of dust needs to be removed here. Thanks for reporting!

graik avatar May 16 '23 08:05 graik