Error Message
PermissionError: [Errno 13] Permission denied: 'cctbx.python'
Stacktrace
tmp_environ = None
def test_file_not_exists(tmp_environ):
> cp = run("--HKLIN " + str(config("foo.mtz")) + ""
" --XYZIN " + str(config("mdm2_1-60A.pdb")) + ""
" -i 2" + ""
" -r " + RES_SHELLS_GOOD + ""
" -p file_not_exists")
/Users/Shared/ccb63/Jenkins/workspace/CCP4/Darwin-clang-pyside2-m1/devtools/test-install/test/pairef/test/test_initial.py:40:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/Users/Shared/ccb63/Jenkins/workspace/CCP4/Darwin-clang-pyside2-m1/devtools/test-install/test/pairef/test/helper.py:31: in run
process = subprocess.Popen(command,
/Users/Shared/ccb63/Jenkins/workspace/CCP4/Darwin-clang-pyside2-m1/devtools/test-install/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py:951: in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Popen: returncode: 255 args: ['cctbx.python', '-m', 'pairef', '--HKLIN', '/...>
args = ['cctbx.python', '-m', 'pairef', '--HKLIN', '/Users/Shared/ccb63/Jenkins/workspace/CCP4/Darwin-clang-pyside2-m1/devtools/test-install/test/pairef/test/fixtures/foo.mtz', '--XYZIN', ...]
executable = b'cctbx.python', preexec_fn = None, close_fds = True, pass_fds = ()
cwd = None, env = None, startupinfo = None, creationflags = 0, shell = False
p2cread = -1, p2cwrite = -1, c2pread = 16, c2pwrite = 17, errread = 18
errwrite = 19, restore_signals = True, gid = None, gids = None, uid = None
umask = -1, start_new_session = False
def _execute_child(self, args, executable, preexec_fn, close_fds,
pass_fds, cwd, env,
startupinfo, creationflags, shell,
p2cread, p2cwrite,
c2pread, c2pwrite,
errread, errwrite,
restore_signals,
gid, gids, uid, umask,
start_new_session):
"""Execute program (POSIX version)"""
if isinstance(args, (str, bytes)):
args = [args]
elif isinstance(args, os.PathLike):
if shell:
raise TypeError('path-like args is not allowed when '
'shell is true')
args = [args]
else:
args = list(args)
if shell:
# On Android the default shell is at '/system/bin/sh'.
unix_shell = ('/system/bin/sh' if
hasattr(sys, 'getandroidapilevel') else '/bin/sh')
args = [unix_shell, "-c"] + args
if executable:
args[0] = executable
if executable is None:
executable = args[0]
sys.audit("subprocess.Popen", executable, args, cwd, env)
if (_USE_POSIX_SPAWN
and os.path.dirname(executable)
and preexec_fn is None
and not close_fds
and not pass_fds
and cwd is None
and (p2cread == -1 or p2cread > 2)
and (c2pwrite == -1 or c2pwrite > 2)
and (errwrite == -1 or errwrite > 2)
and not start_new_session
and gid is None
and gids is None
and uid is None
and umask < 0):
self._posix_spawn(args, executable, env, restore_signals,
p2cread, p2cwrite,
c2pread, c2pwrite,
errread, errwrite)
return
orig_executable = executable
# For transferring possible exec failure from child to parent.
# Data format: "exception name:hex errno:description"
# Pickle is not used; it is complex and involves memory allocation.
errpipe_read, errpipe_write = os.pipe()
# errpipe_write must not be in the standard io 0, 1, or 2 fd range.
low_fds_to_close = []
while errpipe_write < 3:
low_fds_to_close.append(errpipe_write)
errpipe_write = os.dup(errpipe_write)
for low_fd in low_fds_to_close:
os.close(low_fd)
try:
try:
# We must avoid complex work that could involve
# malloc or free in the child process to avoid
# potential deadlocks, thus we do all this here.
# and pass it to fork_exec()
if env is not None:
env_list = []
for k, v in env.items():
k = os.fsencode(k)
if b'=' in k:
raise ValueError("illegal environment variable name")
env_list.append(k + b'=' + os.fsencode(v))
else:
env_list = None # Use execv instead of execve.
executable = os.fsencode(executable)
if os.path.dirname(executable):
executable_list = (executable,)
else:
# This matches the behavior of os._execvpe().
executable_list = tuple(
os.path.join(os.fsencode(dir), executable)
for dir in os.get_exec_path(env))
fds_to_keep = set(pass_fds)
fds_to_keep.add(errpipe_write)
self.pid = _posixsubprocess.fork_exec(
args, executable_list,
close_fds, tuple(sorted(map(int, fds_to_keep))),
cwd, env_list,
p2cread, p2cwrite, c2pread, c2pwrite,
errread, errwrite,
errpipe_read, errpipe_write,
restore_signals, start_new_session,
gid, gids, uid, umask,
preexec_fn)
self._child_created = True
finally:
# be sure the FD is closed no matter what
os.close(errpipe_write)
self._close_pipe_fds(p2cread, p2cwrite,
c2pread, c2pwrite,
errread, errwrite)
# Wait for exec to fail or succeed; possibly raising an
# exception (limited in size)
errpipe_data = bytearray()
while True:
part = os.read(errpipe_read, 50000)
errpipe_data += part
if not part or len(errpipe_data) > 50000:
break
finally:
# be sure the FD is closed no matter what
os.close(errpipe_read)
if errpipe_data:
try:
pid, sts = os.waitpid(self.pid, 0)
if pid == self.pid:
self._handle_exitstatus(sts)
else:
self.returncode = sys.maxsize
except ChildProcessError:
pass
try:
exception_name, hex_errno, err_msg = (
errpipe_data.split(b':', 2))
# The encoding here should match the encoding
# written in by the subprocess implementations
# like _posixsubprocess
err_msg = err_msg.decode()
except ValueError:
exception_name = b'SubprocessError'
hex_errno = b'0'
err_msg = 'Bad exception data from child: {!r}'.format(
bytes(errpipe_data))
child_exception_type = getattr(
builtins, exception_name.decode('ascii'),
SubprocessError)
if issubclass(child_exception_type, OSError) and hex_errno:
errno_num = int(hex_errno, 16)
child_exec_never_called = (err_msg == "noexec")
if child_exec_never_called:
err_msg = ""
# The error must be from chdir(cwd).
err_filename = cwd
else:
err_filename = orig_executable
if errno_num != 0:
err_msg = os.strerror(errno_num)
> raise child_exception_type(errno_num, err_msg, err_filename)
E PermissionError: [Errno 13] Permission denied: 'cctbx.python'
/Users/Shared/ccb63/Jenkins/workspace/CCP4/Darwin-clang-pyside2-m1/devtools/test-install/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py:1821: PermissionError