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perrygeo
concorde not found on path, permissions issue?
Dear Matt,
Thanks for you prompt answer. Now compilation went fine, but I am getting this error when running test_concorde.py:
4c244:tests lquesada$ python test_concorde.py
Traceback (most recent call last):
File "test_concorde.py", line 1, in
Cheers, Luis
The previous one was not really an issue, but this one is: pyconcorde is telling me that concorde is not in my path. But as you can see below it is since I can call it directly.
4c244:pyconcorde-master lquesada$ py.test ======================================== test session starts ======================================== platform darwin -- Python 2.7.10, pytest-2.8.3, py-1.4.31, pluggy-0.3.1 rootdir: /Users/lquesada/Downloads/pyconcorde-master, inifile: collected 0 items / 1 errors
============================================== ERRORS ===============================================
______________________________ ERROR collecting tests/test_concorde.py ______________________________
tests/test_concorde.py:4: in
More over if I set the env var directly it I can go a bit further but face another issue:
4c244:pyconcorde-master lquesada$ py.test ======================================== test session starts ======================================== platform darwin -- Python 2.7.10, pytest-2.8.3, py-1.4.31, pluggy-0.3.1 rootdir: /Users/lquesada/Downloads/pyconcorde-master, inifile: collected 1 items
tests/test_concorde.py F
============================================= FAILURES ============================================== _____________________________________________ test_tour _____________________________________________
matrix = [[0, 791051, 786792, 87405, 839957, 52060, ...], [792333, 0, 41769, 735958, 129216, 741642, ...], [788130, 41769, 0, 7...62, 38822, ...], [842007, 129700, 163828, 785633, 0, 791316, ...], [52105, 741466, 737208, 38942, 790373, 0, ...], ...]
def test_tour(matrix):
matrix_sym = atsp_tsp(matrix, strategy="avg")
outf = "/tmp/myroute.tsp"
with open(outf, 'w') as dest:
dest.write(dumps_matrix(matrix_sym, name="My Route"))
tour = run_concorde(outf, start=10)
/Users/lquesada/Downloads/pyconcorde-master/tests/test_concorde.py:19:
/Users/lquesada/Downloads/pyconcorde-master/pyconcorde/init.py:73: in run_concorde output = subprocess.check_output([CONCORDE, tsp_path], shell=False) /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py:566: in check_output process = Popen(stdout=PIPE, _popenargs, *_kwargs) /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py:710: in init errread, errwrite)
self = <subprocess.Popen object at 0x10d776dd0> args = ['/Users/lquesada/concorde/concorde/TSP/', '/tmp/myroute.tsp'] executable = '/Users/lquesada/concorde/concorde/TSP/', preexec_fn = None, close_fds = False cwd = None, env = None, universal_newlines = False, startupinfo = None, creationflags = 0 shell = False, to_close = set([9]), p2cread = None, p2cwrite = None, c2pread = 9, c2pwrite = 11 errread = None, errwrite = None
def _execute_child(self, args, executable, preexec_fn, close_fds,
cwd, env, universal_newlines,
startupinfo, creationflags, shell, to_close,
p2cread, p2cwrite,
c2pread, c2pwrite,
errread, errwrite):
"""Execute program (POSIX version)"""
if isinstance(args, types.StringTypes):
args = [args]
else:
args = list(args)
if shell:
args = ["/bin/sh", "-c"] + args
if executable:
args[0] = executable
if executable is None:
executable = args[0]
def _close_in_parent(fd):
os.close(fd)
to_close.remove(fd)
# For transferring possible exec failure from child to parent
# The first char specifies the exception type: 0 means
# OSError, 1 means some other error.
errpipe_read, errpipe_write = self.pipe_cloexec()
try:
try:
gc_was_enabled = gc.isenabled()
# Disable gc to avoid bug where gc -> file_dealloc ->
# write to stderr -> hang. http://bugs.python.org/issue1336
gc.disable()
try:
self.pid = os.fork()
except:
if gc_was_enabled:
gc.enable()
raise
self._child_created = True
if self.pid == 0:
# Child
try:
# Close parent's pipe ends
if p2cwrite is not None:
os.close(p2cwrite)
if c2pread is not None:
os.close(c2pread)
if errread is not None:
os.close(errread)
os.close(errpipe_read)
# When duping fds, if there arises a situation
# where one of the fds is either 0, 1 or 2, it
# is possible that it is overwritten (#12607).
if c2pwrite == 0:
c2pwrite = os.dup(c2pwrite)
if errwrite == 0 or errwrite == 1:
errwrite = os.dup(errwrite)
# Dup fds for child
def _dup2(a, b):
# dup2() removes the CLOEXEC flag but
# we must do it ourselves if dup2()
# would be a no-op (issue #10806).
if a == b:
self._set_cloexec_flag(a, False)
elif a is not None:
os.dup2(a, b)
_dup2(p2cread, 0)
_dup2(c2pwrite, 1)
_dup2(errwrite, 2)
# Close pipe fds. Make sure we don't close the
# same fd more than once, or standard fds.
closed = { None }
for fd in [p2cread, c2pwrite, errwrite]:
if fd not in closed and fd > 2:
os.close(fd)
closed.add(fd)
if cwd is not None:
os.chdir(cwd)
if preexec_fn:
preexec_fn()
# Close all other fds, if asked for - after
# preexec_fn(), which may open FDs.
if close_fds:
self._close_fds(but=errpipe_write)
if env is None:
os.execvp(executable, args)
else:
os.execvpe(executable, args, env)
except:
exc_type, exc_value, tb = sys.exc_info()
# Save the traceback and attach it to the exception object
exc_lines = traceback.format_exception(exc_type,
exc_value,
tb)
exc_value.child_traceback = ''.join(exc_lines)
os.write(errpipe_write, pickle.dumps(exc_value))
# This exitcode won't be reported to applications, so it
# really doesn't matter what we return.
os._exit(255)
# Parent
if gc_was_enabled:
gc.enable()
finally:
# be sure the FD is closed no matter what
os.close(errpipe_write)
# Wait for exec to fail or succeed; possibly raising exception
# Exception limited to 1M
data = _eintr_retry_call(os.read, errpipe_read, 1048576)
finally:
if p2cread is not None and p2cwrite is not None:
_close_in_parent(p2cread)
if c2pwrite is not None and c2pread is not None:
_close_in_parent(c2pwrite)
if errwrite is not None and errread is not None:
_close_in_parent(errwrite)
# be sure the FD is closed no matter what
os.close(errpipe_read)
if data != "":
try:
_eintr_retry_call(os.waitpid, self.pid, 0)
except OSError as e:
if e.errno != errno.ECHILD:
raise
child_exception = pickle.loads(data)
raise child_exceptionE OSError: [Errno 13] Permission denied
/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py:1335: OSError ===================================== 1 failed in 0.31 seconds ====================================== 4c244:pyconcorde-master lquesada$
