Issue 36079: pdb on setuptools "ValueError: underlying buffer has been detached" (original) (raw)

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)()
-> """
(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 "", line 1, in
File "/panfs/e/vol0/gholl/checkouts/python-hdf4/setup.py", line 11, in
"""
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 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 "", line 1, in File "/panfs/e/vol0/gholl/checkouts/python-hdf4/setup.py", line 11, in """ 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 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 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