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DFKI-NLP / sherlock

State-of-the-art Information Extraction
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pip install . fails because of jsonnet #31

Closed GabrielKP closed 3 years ago

GabrielKP commented 3 years ago

I following error ERROR when installing the package into a conda environment (python 3.7.11, Ubuntu 20.04):

Building wheel for jsonnet (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/gakr01/.conda/envs/sherlock/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py'"'"'; __file__='"'"'/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-spafaoqr                                                 
       cwd: /tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/                                                                                                                                                                                                
  Complete output (33 lines):                                                                                                                                                                                                                                                  
  running bdist_wheel                                                                                                                                                                                                                                                          
  running build                                                                                                                                                                                                                                                                
  running build_ext                                                                                                                                                                                                                                                            
  g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json core/desugarer.cpp -o core/desugarer.o                                                                                                            
  make: g++: Kommando nicht gefunden                                                                                                                                                                                                                                           
  make: *** [Makefile:161: core/desugarer.o] Fehler 127                                                                                                                                                                                                                        
  Traceback (most recent call last):                                                                                                                                                                                                                                           
    File "<string>", line 1, in <module>                                                                                                                                                                                                                                       
    File "/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py", line 75, in <module>                                                                                                                                                                   
      test_suite="python._jsonnet_test",                                                                                                                                                                                                                                       
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/site-packages/setuptools/__init__.py", line 153, in setup                                                                                                                                                            
      return distutils.core.setup(**attrs)                                                                                                                                                                                                                                     
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/core.py", line 148, in setup                                                                                                                                                                               
      dist.run_commands()                                                                                                                                                                                                                                                      
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/dist.py", line 966, in run_commands                                                                                                                                                                        
      self.run_command(cmd)                                                                                                                                                                                                                                                    
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/dist.py", line 985, in run_command                                                                                                                                                                         
      cmd_obj.run()                                                                                                                                                                                                                                                            
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/site-packages/wheel/bdist_wheel.py", line 299, in run                                                                                                                                                                
      self.run_command('build')                                                                                                                                                                                                                                                
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/cmd.py", line 313, in run_command                                                                                                                                                                          
      self.distribution.run_command(command)                                                                                                                                                                                                                                   
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/dist.py", line 985, in run_command                                                                                                                                                                         
      cmd_obj.run()                                                                                                                                                                                                                                                            
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/command/build.py", line 135, in run                                                                                                                                                                        
      self.run_command(cmd_name)                                                                                                                                                                                                                                               
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/cmd.py", line 313, in run_command                                                                                                                                                                          
      self.distribution.run_command(command)                                                                                                                                                                                                                                   
    File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/dist.py", line 985, in run_command                                                                                                                                                                         
      cmd_obj.run()                                                                                                                                                                                                                                                            
    File "/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py", line 54, in run                                                                                                                                                                        
      raise Exception('Could not build %s' % (', '.join(LIB_OBJECTS)))                                                                                                                                                                                                         
  Exception: Could not build core/desugarer.o, core/formatter.o, core/libjsonnet.o, core/lexer.o, core/parser.o, core/pass.o, core/static_analysis.o, core/string_utils.o, core/vm.o, third_party/md5/md5.o                                                                    
  ----------------------------------------                                                                                                                                                                                                                                     
  ERROR: Failed building wheel for jsonnet
  Running setup.py clean for jsonnet
  Building wheel for seqeval (setup.py) ... done
  Created wheel for seqeval: filename=seqeval-1.2.2-py3-none-any.whl size=16181 sha256=786bf7baf98e8dd82cfb72497374a0606af925b94b5c3ada1e98991b25787cc8
  Stored in directory: /home/gakr01/.cache/pip/wheels/05/96/ee/7cac4e74f3b19e3158dce26a20a1c86b3533c43ec72a549fd7
Successfully built sherlock seqeval
Failed to build jsonnet
Installing collected packages: zipp, typing-extensions, six, urllib3, python-dateutil, jmespath, importlib-metadata, numpy, murmurhash, MarkupSafe, cymem, click, catalogue, botocore, Werkzeug, wasabi, typer, tqdm, threadpoolctl, srsly, smart-open, scipy, s3transfer, regex, pyparsing, pydantic, preshed, joblib, Jinja2, itsdangerous, idna, charset-normalizer, blis, zope.interface, zope.event, tokenizers, thinc, spacy-loggers, spacy-legacy, sentencepiece, scikit-learn, sacremoses, requests, pathy, packaging, langcodes, greenlet, flask, filelock, boto3, transformers, torch, spacy, seqeval, registrable, jsonnet, gevent, flask-cors, sherlock
    Running setup.py install for jsonnet ... error
    ERROR: Command errored out with exit status 1:
     command: /home/gakr01/.conda/envs/sherlock/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py'"'"'; __file__='"'"'/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-qc8xaram/install-record.txt --single-version-externally-managed --compile --install-headers /home/gakr01/.conda/envs/sherlock/include/python3.7m/jsonnet                                                                                                                                                                           
         cwd: /tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/                                                                                                                                                                                              
    Complete output (35 lines):                                                                                                                                                                                                                                                
    running install                                                                                                                                                                                                                                                            
    running build                                                                                                                                                                                                                                                              
    running build_ext                                                                                                                                                                                                                                                          
    g++ -c -g -O3 -Wall -Wextra -Woverloaded-virtual -pedantic -std=c++0x -fPIC -Iinclude -Ithird_party/md5 -Ithird_party/json core/desugarer.cpp -o core/desugarer.o                                                                                                          
    make: g++: Kommando nicht gefunden                                                                                                                                                                                                                                         
    make: *** [Makefile:161: core/desugarer.o] Fehler 127                                                                                                                                                                                                                      
    Traceback (most recent call last):                                                                                                                                                                                                                                         
      File "<string>", line 1, in <module>                                                                                                                                                                                                                                     
      File "/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py", line 75, in <module>                                                                                                                                                                 
        test_suite="python._jsonnet_test",                                                                                                                                                                                                                                     
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/site-packages/setuptools/__init__.py", line 153, in setup                                                                                                                                                          
        return distutils.core.setup(**attrs)                                                                                                                                                                                                                                   
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/core.py", line 148, in setup                                                                                                                                                                             
        dist.run_commands()                                                                                                                                                                                                                                                    
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/dist.py", line 966, in run_commands                                                                                                                                                                      
        self.run_command(cmd)                                                                                                                                                                                                                                                  
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/dist.py", line 985, in run_command                                                                                                                                                                       
        cmd_obj.run()                                                                                                                                                                                                                                                          
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/site-packages/setuptools/command/install.py", line 61, in run                                                                                                                                                      
        return orig.install.run(self)                                                                                                                                                                                                                                          
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/command/install.py", line 545, in run                                                                                                                                                                    
        self.run_command('build')                                                                                                                                                                                                                                              
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/cmd.py", line 313, in run_command                                                                                                                                                                        
        self.distribution.run_command(command)                                                                                                                                                                                                                                 
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/dist.py", line 985, in run_command                                                                                                                                                                       
        cmd_obj.run()                                                                                                                                                                                                                                                          
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/command/build.py", line 135, in run                                                                                                                                                                      
        self.run_command(cmd_name)                                                                                                                                                                                                                                             
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/cmd.py", line 313, in run_command                                                                                                                                                                        
        self.distribution.run_command(command)                                                                                                                                                                                                                                 
      File "/home/gakr01/.conda/envs/sherlock/lib/python3.7/distutils/dist.py", line 985, in run_command                                                                                                                                                                       
        cmd_obj.run()                                                                                                                                                                                                                                                          
      File "/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py", line 54, in run                                                                                                                                                                      
        raise Exception('Could not build %s' % (', '.join(LIB_OBJECTS)))                                                                                                                                                                                                       
    Exception: Could not build core/desugarer.o, core/formatter.o, core/libjsonnet.o, core/lexer.o, core/parser.o, core/pass.o, core/static_analysis.o, core/string_utils.o, core/vm.o, third_party/md5/md5.o                                                                  
    ----------------------------------------                                                                                                                                                                                                                                   
ERROR: Command errored out with exit status 1: /home/gakr01/.conda/envs/sherlock/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py'"'"'; __file__='"'"'/tmp/pip-install-dtcnya31/jsonnet_ec2de8e1b63643d891bff9bb3a88b388/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-qc8xaram/install-record.txt --single-version-externally-managed --compile --install-headers /home/gakr01/.conda/envs/sherlock/include/python3.7m/jsonnet Check the logs for full command output.

This can be circumvented by installing jsonnet manually:

conda install -c conda-forge jsonnet

This needs to be checked for:

  1. venv installations
  2. plain installations
  3. On other systems

And then has to be fixed.

GabrielKP commented 3 years ago

This seems to be related to the conda version: conda 4.10 seems to work, but 4.9 or 4.8 do not. Would be cool if somebody can confirm if it works for them without issues. @leonhardhennig