Error freezing h5py 2.4 with cx_freeze 4.3.1
I am trying to freeze a Python script using cx_Freeze. The script uses h5py v2.4.0b1. When I run the executable file created by cx_Freeze I get the following Traceback:
Traceback (most recent call last):
File "C:\Python34\lib\site-packages\cx_Freeze\initscripts\Console.py", line 27, in <module>
exec(code, m.__dict__)
File "main.py", line 7, in <module>
from xman import xmanLogging, xmanManager, xmanInfo
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2237, in _find_and_load
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2226, in _find_and_load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1191, in _load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1161, in _load_backward_compatible
File "d:\user\aagbds\Programmierung\Python\EclipseProjects\xMAN\src\xman\__init__.py", line 3, in <
module>
from .xmlHandler import barMAN, xmlClass
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2237, in _find_and_load
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2226, in _find_and_load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1191, in _load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1161, in _load_backward_compatible
File "d:\user\aagbds\Programmierung\Python\EclipseProjects\xMAN\src\xman\xmlHandler\__init__.py", l
ine 7, in <module>
from . import barMAN, xmlClass
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2284, in _handle_fromlist
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 321, in _call_with_frames_removed
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2237, in _find_and_load
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2226, in _find_and_load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1191, in _load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1161, in _load_backward_compatible
File "d:\user\aagbds\Programmierung\Python\EclipseProjects\xMAN\src\xman\xmlHandler\xmlClass.py", l
ine 25, in <module>
from xman.COMInterface import COMmanager
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2237, in _find_and_load
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2226, in _find_and_load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1191, in _load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1161, in _load_backward_compatible
File "d:\user\aagbds\Programmierung\Python\EclipseProjects\xMAN\src\xman\COMInterface\__init__.py",
line 7, in <module>
from . import COMmanager
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2284, in _handle_fromlist
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 321, in _call_with_frames_removed
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2237, in _find_and_load
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2226, in _find_and_load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1191, in _load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1161, in _load_backward_compatible
File "d:\user\aagbds\Programmierung\Python\EclipseProjects\xMAN\src\xman\COMInterface\COMmanager.py
", line 20, in <module>
import logging, win32com.client , pythoncom, pywintypes, h5py, \
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2237, in _find_and_load
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 2226, in _find_and_load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1191, in _load_unlocked
File "X:\Python34-x32\lib\importlib\_bootstrap.py", line 1161, in _load_backward_compatible
File "C:\Python34\lib\site-packages\h5py\__init__.py", line 10, in <module>
from h5py import _errors
ImportError: cannot import name '_errors'
I am using Python 3.4.2 - 32 bit. Anyone have an idea?
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1 answer
I spent two days trying to figure this out.
I am using python 2.7 64-bit but I got the same error as windows, ubuntu 14 and mac os 10.9 and 10.10. I am also using h5py 2.4.0 and cx_Freeze 4.3.4.
The solution for me was as follows:
I had to change the hooks.py in cx_Freeze for load_h5py so that:
def load_h5py(finder, module):
"""h5py module has a number of implicit imports"""
finder.IncludeModule('h5py.defs')
finder.IncludeModule('h5py.utils')
finder.IncludeModule('h5py._proxy')
try:
finder.IncludeModule('h5py._errors')
finder.IncludeModule('h5py.h5ac')
except:
pass
try:
finder.IncludeModule('h5py.api_gen')
except:
pass
Also, it seems that some of the h5py. *, so links to links with
@ loader_path / .dylibs / libhdf5.8.dylib
This is not overwritten by cx_freeze.
I had to change the code in cx_freeze (actually, I copied the code into my setup.py and just called it right after calling the main setup (....) to send all files in the assembly)
# this is a straight copy paste from macdist.py in the cx_Freeze code
def setRelativeReferencePaths(binDir):
""" For all files in Contents/MacOS, check if they are binaries
with references to other files in that dir. If so, make those
references relative. The appropriate commands are applied to all
files; they will just fail for files on which they do not apply."""
files = []
for root, dirs, dir_files in os.walk(binDir):
files.extend([os.path.join(root, f).replace(binDir + "/", "")
for f in dir_files])
for fileName in files:
# install_name_tool can't handle zip files or directories
filePath = os.path.join(binDir, fileName)
if fileName.endswith('.zip'):
continue
# ensure write permissions
mode = os.stat(filePath).st_mode
if not (mode & stat.S_IWUSR):
os.chmod(filePath, mode | stat.S_IWUSR)
# let the file itself know its place
subprocess.call(('install_name_tool', '-id',
'@executable_path/' + fileName, filePath))
# find the references: call otool -L on the file
otool = subprocess.Popen(('otool', '-L', filePath),
stdout=subprocess.PIPE)
references = otool.stdout.readlines()[1:]
for reference in references:
# find the actual referenced file name
referencedFile = reference.decode().strip().split()[0]
if referencedFile.startswith('@loader_path/.dylibs/'):
# this file is likely an hdf5 file
print "Found hdf5 file {} referencing {}".format(filePath, referencedFile)
elif referencedFile.startswith('@'):
# the referencedFile is already a relative path
continue
path, name = os.path.split(referencedFile)
# some referenced files have not previously been copied to the
# executable directory - the assumption is that you don't need
# to copy anything fro /usr or /System, just from folders like
# /opt this fix should probably be elsewhere though
# if (name not in files and not path.startswith('/usr') and not
# path.startswith('/System')):
# print(referencedFile)
# self.copy_file(referencedFile,
# os.path.join(self.binDir, name))
# files.append(name)
# see if we provide the referenced file;
# if so, change the reference
if name in files:
newReference = '@executable_path/' + name
subprocess.call(('install_name_tool', '-change',
referencedFile, newReference, filePath))
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