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pdb on setuptools "ValueError: underlying buffer has been detached" #80260

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gerritholl mannequin opened this issue Feb 22, 2019 · 1 comment
Open

pdb on setuptools "ValueError: underlying buffer has been detached" #80260

gerritholl mannequin opened this issue Feb 22, 2019 · 1 comment
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stdlib Python modules in the Lib dir

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@gerritholl
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Mannequin

gerritholl mannequin commented Feb 22, 2019

BPO 36079
Nosy @gerritholl

Note: these values reflect the state of the issue at the time it was migrated and might not reflect the current state.

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GitHub fields:

assignee = None
closed_at = None
created_at = <Date 2019-02-22.14:42:18.620>
labels = []
title = 'pdb on setuptools "ValueError: underlying buffer has been detached"'
updated_at = <Date 2019-02-22.14:42:18.620>
user = 'https://github.com/gerritholl'

bugs.python.org fields:

activity = <Date 2019-02-22.14:42:18.620>
actor = 'Gerrit.Holl'
assignee = 'none'
closed = False
closed_date = None
closer = None
components = []
creation = <Date 2019-02-22.14:42:18.620>
creator = 'Gerrit.Holl'
dependencies = []
files = []
hgrepos = []
issue_num = 36079
keywords = []
message_count = 1.0
messages = ['336316']
nosy_count = 1.0
nosy_names = ['Gerrit.Holl']
pr_nums = []
priority = 'normal'
resolution = None
stage = None
status = 'open'
superseder = None
type = None
url = 'https://bugs.python.org/issue36079'
versions = ['Python 3.6']
@gerritholl
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gerritholl mannequin commented Feb 22, 2019

I am unable to use pdb to debug a problem I have with the python-hdf4 installer. The exception in the program to be debugged is printed twice, followed by an exception in pdb itself, ending with ValueError: underlying buffer has been detached. See below, in particular the lower part:

$ python -mpdb setup.py install
python -mpdb setup.py install                                                                                            
> /panfs/e/vol0/gholl/checkouts/python-hdf4/setup.py(11)<module>()                                                       
-> """                                                                                                               
(Pdb) cont                                                                                                           
running install                                                                                                              
running bdist_egg                                                                                                            
running egg_info                                                                                                                     
running build_src                                                                                                                    
build_src                                                                                                            
building extension "pyhdf._hdfext" sources                                                                                   
build_src: building npy-pkg config files                                                                                       
writing python_hdf4.egg-info/PKG-INFO                                                                                                
writing dependency_links to python_hdf4.egg-info/dependency_links.txt                                                       
writing top-level names to python_hdf4.egg-info/top_level.txt                                                               
reading manifest file 'python_hdf4.egg-info/SOURCES.txt'                                                                 
writing manifest file 'python_hdf4.egg-info/SOURCES.txt'                                                                       
installing library code to build/bdist.linux-x86_64/egg
running install_lib                                                                                                         
running build_py                                               
running build_ext                                                                                                        
customize UnixCCompiler                                                           
customize UnixCCompiler using build_ext                                                                                                                                                           
building 'pyhdf._hdfext' extension                                                                
compiling C sources                              
C compiler: gcc -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC
                                                                                  
compile options: '-I/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/core/include -I/panfs/e/vol0/gholl/venv/py36/include -I/hpc/rhome/software/python/3.6.5/include/python3.6m -c'
extra options: '-DNOSZIP'                                                               
Traceback (most recent call last):                                                
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 1667, in main                            
    pdb._runscript(mainpyfile)                                                          
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 1548, in _runscript                     
    self.run(statement)                                                                        
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/bdb.py", line 434, in run                              
    exec(cmd, globals, locals)                                                                                
  File "<string>", line 1, in <module>                                                                       
  File "/panfs/e/vol0/gholl/checkouts/python-hdf4/setup.py", line 11, in <module>                            
    """                                                                                            
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/core.py", line 171, in setup
    return old_setup(**new_attr)                                                                                      
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/__init__.py", line 129, in setup
    return distutils.core.setup(**attrs)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 955, in run_commands
    self.run_command(cmd)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/command/install.py", line 62, in run
    r = self.setuptools_run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/command/install.py", line 56, in setuptools_run
    self.do_egg_install()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/command/install.py", line 109, in do_egg_install
    self.run_command('bdist_egg')
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/command/bdist_egg.py", line 172, in run
    cmd = self.call_command('install_lib', warn_dir=0)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/command/bdist_egg.py", line 158, in call_command
    self.run_command(cmdname)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/command/install_lib.py", line 11, in run
    self.build()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/command/install_lib.py", line 107, in build
    self.run_command('build_ext')
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/command/build_ext.py", line 261, in run
    self.build_extensions()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/command/build_ext.py", line 448, in build_extensions
    self._build_extensions_serial()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/command/build_ext.py", line 473, in _build_extensions_serial
    self.build_extension(ext)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/command/build_ext.py", line 379, in build_extension
    **kws)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/ccompiler.py", line 92, in <lambda>
    m = lambda self, *args, **kw: func(self, *args, **kw)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/ccompiler.py", line 363, in CCompiler_compile
    single_compile(o)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/ccompiler.py", line 305, in single_compile
    if not _needs_build(obj, cc_args, extra_postargs, pp_opts):
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/ccompiler.py", line 64, in _needs_build
    last_cmdline = lines[-1]
IndexError: list index out of range
Uncaught exception. Entering post mortem debugging
Running 'cont' or 'step' will restart the program
Traceback (most recent call last):
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 1667, in main
    pdb._runscript(mainpyfile)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 1548, in _runscript
    self.run(statement)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/bdb.py", line 434, in run
    exec(cmd, globals, locals)
  File "<string>", line 1, in <module>
  File "/panfs/e/vol0/gholl/checkouts/python-hdf4/setup.py", line 11, in <module>
    """
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/core.py", line 171, in setup
    return old_setup(**new_attr)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/__init__.py", line 129, in setup
    return distutils.core.setup(**attrs)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 955, in run_commands
    self.run_command(cmd)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/command/install.py", line 62, in run
    r = self.setuptools_run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/command/install.py", line 56, in setuptools_run
    self.do_egg_install()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/command/install.py", line 109, in do_egg_install
    self.run_command('bdist_egg')
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/command/bdist_egg.py", line 172, in run
    cmd = self.call_command('install_lib', warn_dir=0)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/command/bdist_egg.py", line 158, in call_command
    self.run_command(cmdname)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/setuptools/command/install_lib.py", line 11, in run
    self.build()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/command/install_lib.py", line 107, in build
    self.run_command('build_ext')
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/cmd.py", line 313, in run_command
    self.distribution.run_command(command)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/dist.py", line 974, in run_command
    cmd_obj.run()
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/command/build_ext.py", line 261, in run
    self.build_extensions()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/command/build_ext.py", line 448, in build_extensions
    self._build_extensions_serial()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/distutils/command/build_ext.py", line 473, in _build_extensions_serial
    self.build_extension(ext)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/command/build_ext.py", line 379, in build_extension
    **kws)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/ccompiler.py", line 92, in <lambda>
    m = lambda self, *args, **kw: func(self, *args, **kw)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/ccompiler.py", line 363, in CCompiler_compile
    single_compile(o)
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/ccompiler.py", line 305, in single_compile
    if not _needs_build(obj, cc_args, extra_postargs, pp_opts):
  File "/panfs/e/vol0/gholl/venv/py36/lib/python3.6/site-packages/numpy/distutils/ccompiler.py", line 64, in _needs_build
    last_cmdline = lines[-1]
IndexError: list index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 1694, in <module>
    pdb.main()
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 1686, in main
    pdb.interaction(None, t)
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 351, in interaction
    self.print_stack_entry(self.stack[self.curindex])
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 1453, in print_stack_entry
    self.format_stack_entry(frame_lineno, prompt_prefix))
  File "/hpc/rhome/software/python/3.6.5/lib/python3.6/pdb.py", line 453, in message
    print(msg, file=self.stdout)
ValueError: underlying buffer has been detached

@ezio-melotti ezio-melotti transferred this issue from another repository Apr 10, 2022
@iritkatriel iritkatriel added the stdlib Python modules in the Lib dir label Nov 27, 2023
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