I've been struggling to get pytables and the underlying HDF5 library working on python in OS X, so thought I'd give the Enthought distribution a go (which will also greatly simplify deployment across platforms later on).
I installed EPD 7.3 for 64-bit OS X (I'm running 10.8.2), but unfortunately no success, I get the following when trying to load the pytables...
In [4]: import tables
--------------------------------------------------------------------------- ImportError Traceback (most recent call last) /<ipython-input-4-389ecae14f10> in <module>()
----> 1 import tables
/Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables/__init__.py in <module>()
57
58 # Necessary imports to get versions stored on the Pyrex extension
---> 59 from tables.utilsExtension import getPyTablesVersion, getHDF5Version
60
61 __version__ = getPyTablesVersion()
ImportError: dlopen(/Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables/utilsExtension.so, 2): Symbol not found: _SZ_BufftoBuffCompress Referenced from: /Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables/utilsExtension.so Expected in: flat namespace in /Users/davidperry/Library/Python/2.7/lib/python/site-packages/tables/utilsExtension.so
I presume this means that szip, a required library for HDF5, cannot be found? If it is actually missing from EPD (seems odd...), can I install it myself without building HDF5 from source? Or is is just in a strange place?
First, I apologize for the problems you are encountering.
It looks as if you are not loading pytables from EPD, but from a former installation. How does PYTHONPATH look like in your environment ?
Generally, EPD is installed somewhere in /Library/Frameworks/Python.framework/Versions/7.3. What does the following do ?
PYTHONPATH= /Library/Frameworks/Python.framework/Versions/7.3/bin/python -c "import tables; print tables.__version__"
or (64 bits version):
PYTHONPATH= /Library/Frameworks/EPD64.framework/Versions/7.3/bin/python -c "import tables; print tables.__version__"
It should return you something like "2.3.1" (the actual tables version available in EPD). If that indeed works, then do make EPD the default python in your environment, you will need to adapt the PATH/PYTHONPATH variables to make it available.
If that still does not work, then can you try the following (adapt for 32 bits):
PYTHONPATH= /Library/Frameworks/EPD64.framework/Versions/7.3/bin/python -c "import sys; print sys.path"
and paste the output ?
Related
When importing pyodbc
❯ python
>>> import pyodbc
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: dlopen(/Users/pcosta/Documents/test/myenv/lib/python3.7/site-packages/pyodbc.cpython-37m-darwin.so, 2): Library not loaded: /usr/local/opt/unixodbc/lib/libodbc.2.dylib
Referenced from: /Users/pcosta/Documents/test/myenv/lib/python3.7/site-packages/pyodbc.cpython-37m-darwin.so
Reason: image not found
I know why this is happening, as I don't have libodbc.2.dylib in the expected location. The reason is I do not have permission to write to /usr/local/, so I have Homebrew installing into ~/.brew. This mostly works fine. I am even able to get both tsql and isql working as expected by following the steps outlined here: https://github.com/mkleehammer/pyodbc/wiki/Connecting-to-SQL-Server-from-Mac-OSX.
So I do have libodbc.2.dylib, it's just that it lives in /Users/pcosta/.brew/lib, not /usr/local/opt/unixodbc/lib.
The main questions is can I get pyodbc to look for libodbc.2.dylib (and other associated files) in another directory?
I have all the files needed and have configured them correctly, I just need to repoint pyodbc somehow.
Thanks!
Thanks in part to guidance from this GitHub issue I was able to come to some solution.
Assuming you have brew install unixodbc:
Add the following paths (to .zshrc, .bashrc, or .bash_profile):
export LDFLAGS="-L/Users/pcosta/homebrew/opt/unixodbc/lib $LDFLAGS"
export CPPFLAGS="-I/Users/pcosta/homebrew/opt/unixodbc/include $CPPFLAGS"
export PKG_CONFIG_PATH="/Users/pcosta/homebrew/opt/unixodbc/lib/pkgconfig $PKG_CONFIG_PATH"
Run pip install --no-binary pyodbc pyodbc to bypass the binary and build yourself
I'm trying to import ocrmypdf on my company's client's Windows Server 2016 Build 14393 computer using Python 37-32. When I import the library, in a Jupyter Notebook, it is unable to locate leptonica by using ctypes.utility.find_library().
Ocrmypdf is a Linux-developed Python 3 package. Per the documentation (https://ocrmypdf.readthedocs.io/en/latest/introduction.html) it does not support Windows. The suggested workarounds are a docker container and Windows Subsystem for Linux.
I would rather not use a docker container as neither I nor my coworkers are very experienced with it. I am unable to use wsl as it is not available for my build of Windows Server 2016 (see the troubleshoot subsection: https://learn.microsoft.com/en-us/windows/wsl/install-on-server)
This discussion (find_library() in ctypes) states that you can point ctypes.utility.find_library to the needed library file by editing the environment Path variable to be a folder which includes it. Conveniently, Tesseract OCR's windows download includes liblept. Would editing the Path variable to point toward that folder be a dangerous thing to do?
Edit: I tried adding the path to Tesseract-OCR's folder on my laptop's environment Path and restarted Anaconda, etc. ocrmypdf still gave the same error.
A closer read of that discussion brought up the point that find_library operates differently on Windows. A read of the documentation (https://docs.python.org/2.5/lib/ctypes-finding-shared-libraries.html) states that "On Windows, find_library searches along the system search path, and returns the full pathname, but since there is no predefined naming scheme a call like find_library("c") will fail and return None." Does this mean I have to hardcode in a name to use in order to find the library?
This issue has been replicated, albeit on a different machine, here: https://github.com/jbarlow83/OCRmyPDF/issues/341. You can reproduce the issue by running the below code on a Windows machine.
!pip install ocrmypdf
import ocrmypdf
The expected result of the above code is that ocrmypdf is successfully imported in a usable form.
The result of the above code is:
OSError Traceback (most recent call last)
<ipython-input-2-a81f3474d7ad> in <module>
----> 1 import ocrmypdf
~\AppData\Local\Continuum\anaconda3\lib\site-packages\ocrmypdf\__init__.py in <module>
16 # along with OCRmyPDF. If not, see <http://www.gnu.org/licenses/>.
17
---> 18 from . import helpers, hocrtransform, leptonica, pdfa, pdfinfo
19 from ._version import PROGRAM_NAME, __version__
20 from .api import Verbosity, configure_logging, ocr
~\AppData\Local\Continuum\anaconda3\lib\site-packages\ocrmypdf\leptonica.py in <module>
40 logger = logging.getLogger(__name__)
41
---> 42 lept = ffi.dlopen(find_library('lept'))
43 lept.setMsgSeverity(lept.L_SEVERITY_WARNING)
44
OSError: cannot load library '<None>': error 0x57
I have been able to get this working Windows 10 by updating the path and it works fine. I used msys2 to install it, hence, the path name. Update to point where your liblept-5.dll is located.
if os.name == 'nt':
os.environ['PATH'] = os.environ.get("PATH", "") + ';C:\\msys64\\mingw64\\bin'
I'm trying to build the VTK library with python wrappers. I want to develop a python program to post-process some CFD results in VTK format.
I'm compiling the source in a local folder.
Unfortunately I'm facing several issues: firstly during the compilation I get the following error message:
CMake Error at Common/Core/cmake_install.cmake:47 (file):
file INSTALL cannot find
"/home/riccardo/Software/VTK/build/lib/libvtkCommonCore-8.0.so.1".
I tried to disable the option of shared libraries as suggested here VTK install error cannot find libvtkCommonCore-6.3.so.1
in the cmake configuration
cmake ..\
-DCMAKE_INSTALL_PREFIX=/home/riccardo/Software/VTK/build \
-DBUILD_SHARED_LIBS:BOOL=OFF \
-DCMAKE_BUILD_TYPE=Release \
-DVTK_USE_SYSTEM_ZLIB:BOOL=ON
In this case the compilation went fine but when I tried to import vtk in python I get this error:
from .vtkCommonCore import *
42 from .vtkCommonMath import *
43 from .vtkCommonMisc import *
~/Software/VTK/build/Wrapping/Python/vtk/vtkCommonCore.py in <module>()
7 # during build and testing, the modules will be elsewhere,
8 # e.g. in lib directory or Release/Debug config directories
----> 9 from vtkCommonCorePython import *
ImportError: No module named 'vtkCommonCorePython'
I really don't know how to fix it.
Any help would be more than welcome.
Many thanks in advance!!!
Have you tried to tell CMake the python version you want to wrap?
That is, add:
-D VTK_WRAP_PYTHON:BOOL=ON \
-D VTK_PYTHON_VERSION:STRING=3.5 # or your python version
-D PYTHON_EXECUTABLE:PATH=\usr\bin\python3 # or wherever your python exec is
In the CMake configuration and see what happens.
I am using Anaconda on OS X Mavericks. When I try loading cv2 I get an import error (see below). Do you know how to fix this?
>>import cv2
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: dlopen(/usr/local/Cellar/opencv/2.4.8.2/lib/python2.7/site-packages/cv2.so,
2): Library not loaded: /usr/local/lib/libpng15.15.dylib
Referenced from: /usr/local/Cellar/opencv/2.4.8.2/lib/libopencv_highgui.2.4.dylib
Reason: image not found
I am not sure it's relevant, but in /usr/local/lib/ I have libpng16.16.dylib instead of libpng15.15.dylib.
This is the solution I found:
comment the PYTHONPATH environment in ~/.bash_profile, as suggested by #asmeurer
install opencv using https://binstar.org/jjhelmus/opencv
As suggested in this issue, I fixed this problem by simply executing
conda update hdf5
you could also just add it to your PYTHONPATH. here's how:
you should be able to get it to load through one of the other (non anaconda) python executables. mine were located at:
/usr/bin/python (default system python) and /usr/local/bin/python (brew)
call the python executable using the full path
once you successfully import cv2 run: cv2.__file__
this will give you the file's path which you can then take (full directory path not including filename) and add as the first argument to your PYTHONPATH defined in ~/.bash_profile
after changing the .bash_profile don't forget to run
source ~/.bash_profile to make the changes effective
fire up anaconda python and it should now find cv2
I'm having trouble figuring out an error message in Python.
yesterday, I've installed python using the latest EPD package, and wxPython2.9 using the wxPython2.9-osx-cocoa-py2.7 package for Mac OS.
I then added wx to my PYTHONPATH.
export WXDIR=/usr/local/lib/wxPython-2.9.1.1/lib/python2.7/site-packages/wx-2.9.1-osx_cocoa
export PYTHONPATH=$WXDIR
export PYTHONPATH=$PYTHONPATH:$WXDIR/tools
but when I try to run stuff I get this error:
In [14]: import matplotlib.pyplot
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
/Users/imrisofer/Documents/third/hddm-read-only/hddm/<ipython console> in <module>()
/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/matplotlib/pyplot.py in <module>()
93
94 from matplotlib.backends import pylab_setup
---> 95 new_figure_manager, draw_if_interactive, show = pylab_setup()
96
97 #docstring.copy_dedent(Artist.findobj)
/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/matplotlib/backends/__init__.py in pylab_setup()
23 backend_name = 'matplotlib.backends.%s'%backend_name.lower()
24 backend_mod = __import__(backend_name,
---> 25 globals(),locals(),[backend_name])
26
27 # Things we pull in from all backends
/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/matplotlib/backends/backend_wxagg.py in <module>()
21
22 from backend_agg import FigureCanvasAgg
---> 23 import backend_wx # already uses wxversion.ensureMinimal('2.8')
24 from backend_wx import FigureManager, FigureManagerWx, FigureCanvasWx, \
25 FigureFrameWx, DEBUG_MSG, NavigationToolbar2Wx, error_msg_wx, \
/Library/Frameworks/EPD64.framework/Versions/7.0/lib/python2.7/site-packages/matplotlib/backends/backend_wx.py in <module>()
43 import wxversion
44 except ImportError:
---> 45 raise ImportError(missingwx)
46
47 # Some early versions of wxversion lack AlreadyImportedError.
ImportError: Matplotlib backend_wx and backend_wxagg require wxPython >=2.8
I can successfully import wx, so I don't no what's the problem.
Am I missing anything in the PYTHONPATH?
In Ubuntu 12.04, this problem can be solved by running the command
sudo apt-get install libjpeg62
I realize this may not be useful here, but I wanted to document it somewhere on teh interwebz so I can find it when I run into this problem again myself which will undoubtedly happen.
I'm using Ubuntu 13.10, Canopy 1.2, and PyCharm 3.0.2. When trying to use matlablib, it always complains "Matplotlib backend_wx and backend_wxagg require wxPython >=2.8".Pretty sure that I'm using wxPython 2.8. Then I tried all the methods described in this page, but neither of them works for me.
It turns out that it can be solved by modifying matplotlibrc file. There is a line:
backend : WXAgg
In fact we can change the backend to whatever we like, and I change it to TKAgg, which works just fine for me.
Select your wx version before importing any wx modules
import wxversion
wxversion.select('2.8')
The above code should come before import wx
This happened to me on a Windows x64 installation that did not install wxversion.py in the site-packages directory (c:\Python27\Lib\site-packages by default).
You can get a copy of wxversion.py from the WX svn repository:
http://svn.wxwidgets.org/viewvc/wx/wxPython/trunk/wxversion/wxversion.py?content-type=text%2Fplain&view=co
this link helped me
https://support.enthought.com/entries/22601196-wxPython-2-8-and-2-9
Here's how I fixed the problem, which I hope will be useful for others in future
In Terminal: gedit Enthought/Canopy_64bit/User/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
Edit the line "backend : WXAgg" into "backend : QtAgg"
Save and exit
I just ran into this myself. One potential cause of this (quite unhelpful) error message is if you installed wx as a single-version installation (INSTALL_MULTIVERSION=0 when running setup.py). In this case, the module wxversion does not get built (or installed) and as such matplotlib incorrectly assumes that all of wx is missing.
This currently is the default setting in installations by the homebrew version of wxWidgets (wxmac) with the option --python.
In your case (albeit a year and a half late), you'd need to ensure that wxversion.py exists within /usr/local/lib/wxPython-2.9.1.1/lib/python2.7/site-packages/. If it doesn't, you'd need to recompile wx with the above flag set. Otherwise you just need to set your $PYTHONPATH such that it includes the base site-packages directory, too:
export WXDIR=/usr/local/lib/wxPython-2.9.1.1/lib/python2.7/site-packages
export PYTHONPATH=$WXDIR:$WXDIR/wx-2.9.1-osx_cocoa:$WXDIR/wx-2.9.1-osx_cocoa/tools
I've solved with this:
defaults write com.apple.versioner.python Prefer-32-Bit -bool yes
I solved this by setting the backend to MacOSX in ~/.matplotlib/matplotlibrc:
backend : MacOSX
I've solved this on Windows by looking in the site packages folder in the python library. In there, there should be another folder titled site-packages. In this subfolder, there is the wxversion library. If you copy this library into the Lib folder in python, this import error should be averted.
sudo apt-get install python-wxtools
Install it. Worked for me.