I have the following issue: I have installed anaconda 3 and installed a package called "pygrib" into my anaconda environment. Now when importing pygrib in a file in my environment, it will show me this error:
import pygrib
ImportError: libhdf5.so.10: cannot open shared object file: No such file or directory
As I am a noobie, I dont really know what to do with this information. I installed the h5py package and some other related ones, but it didnt resolve the issue. What to do?
This is a linking error with the HDF5 library. Are you building pygrib from source or using the conda-forge channel to install it via conda? When I use the conda-forge build of pygrib I get the same issue. The GRIB API from ECMWF (on conda-forge it is listed as ecmwf_grib) is what pygrib depends on and the HDF5 dependency comes from netCDF4 being used in the GRIB API library. Specifically, using the latest HDF5 (1.10.0 at this time) is what is causing a problem. Using HDF5 1.8.* instead allows pygrib to import properly.
To force conda to grab a specific version, just do:
conda install pygrib hdf5=1.8
This will get conda to solve the package specifications again with the older HDF5 library and likely clear up the issue. This assumes you are in the conda environment that you installed pygrib into. You could also create a new environment with conda create -n <env name> pygrib hdf5=1.8 if you wanted to.
In general, when you see these errors where a library is not found, it is often a matter of getting the right version of a library installed. With conda, this sort of thing happens when updating packages and a newer version of a library gets installed that a package you are using has not been properly linked with. As long as you can track down the package/library that is causing trouble, you can use the above procedure to start requiring certain versions of things get installed and conda should then update or downgrade things so that things work together again. Hopefully this makes sense and helps.
This part may or may not interest you, but what I cannot say for certain is where this problem originates. My guess is that it is something with ecmwf_grib and how it is built. That is where ldd shows the old HDF5 dependency showing up for my installation. If I can figure out the exact issue, I'll update this answer.
Related
I am using a Jupyter notebook running in VSCode to test some ideas for a work project and I am using a package that is in a private GitHub repo. I encountered certain conflicts with versions of jax and numpy and after some fiddling trying to fix the issues, I simply re-installed said package to make sure I was using the correct versions of all required packages. Everything seemed fine until I re-opened the notebook and found a bunch of Import "<package name>" could not be resolved Pylance.
The imports still work and the code runs, however, PyLance appears not to be "seeing" said package.
I am using a conda Python 3.8 environment and to re-install the package I ran
pip install -e . --force-reinstall
I have also tried un-installing and re-installing the package, as well as creating a brand new conda env, and then installing the package there. Neither of these options worked however and I was stuck with the same issue.
Upon inspection of what is in sys.path I saw a strange entry
'__editable__.<package_name>-<package_version>.finder.__path_hook__'
I know that a colleague (who does not have this issue) does not see anything similar and instead has the correct local path to the package.
I should also note that I have the Python extension enabled, which includes the Jupyter and Pylance extensions as well. I have tried re-installing those extensions as well and that did not solve the issue either.
Edit.
I will add that I only get this PyLance error in notebooks. If I open a regular Python file then all PyLance features appear to be working as expected.
On attempting to use package control to install EasyClangComplete in sublime text 3 on gentoo, I got the following error:
Package Control: The dependency 'pygments' is not currently installed; installing...
Package Control: The dependency 'pygments' is not available
Package Control: The dependency 'pygments' could not be installed or updated
I have pygments installed (dev-python/pygments), and I have also tried installing it using pip (No difference).
In the console, I got this for the sys.path
['/opt/sublime-text3', '/opt/sublime-text3/python3.3.zip', '/home/username/.config/sublime-text-3/Lib/python3.3', '/home/username/.config/sublime-text-3/Packages']
Whereas the pygments module has installed under /usr/lib/python3.9/site-packages.
I don't have python 3.3 installed on this machine, so I guess that sublime comes with it. I tried pasting the 3.9 package into the sys.path locations regardless, no difference.
I have looked online for other people with this error, only to find people from 2018 who had problems with sublime text dealing with TLS. This is not the same thing. I also think it's probably not an issue with package control or easyclangcomplete, or else I would have been able to find this issue with the keywords I've searched.
Suddenly, it seems to work now.
I've done a full system update(Upgraded packages including python 3.8 and 3.9, although I updated sublime text before that to no effect), and restarted everything(Which I had tried before withhout effect), but other than that I can't see why it can find and install pygments now whereas it couldn't before.
I am using Pythonista for iOS and installed the cryptography package using the latest version of StaSh. It looked like there was an issue during installation but it still seemed to be successful:
Extracting archive file ...
Archive extracted.
Running setup file ...
TypeError('expected string or bytes-like object',)
Failed to run setup.py
Fall back to directory guessing ...
Package installed: cryptography
However, when I try to import Fertnet from cryptography.fertnet I get a ModuleNotFoundError. Apparently I'm missing cryptography.hazmat.bindings._padding. Does anyone have any idea why I'm not getting that module?
The cryptography module is partly written in C.
Those parts have to be compiled into shared libraries. The libraries are named _constant_time, _openssl and _padding and they should be located in hazmat/bindings.
AFAICT PyPI only carries compiled packages for linux, windows and macOS but not for IOS.
So my guess is that setup.py fails because it cannot compile those libraries.
I'm having an error running simple code using cv2 module.
It's just:
import cv2
img = cv2.imread('sudoku.png',0)
cv2.imshow('image',img)
And it fails with the following error:
QObject::moveToThread: Current thread (0x1b74720) is not the object's thread (0x1e57d70).
Cannot move to target thread (0x1b74720)
I googled this error and tried a lot of things but it doesn't help. I tried installing without pip, I tried using step-by-step installation (from official OpenCV) but nothing helps.
When I run:
cv2.__version__
It returns 3.4.3
As noted already, the basis for this problem is discussed in opencv-python issue 46, and results from the duplication of the following libraries both on the host and the opencv-python distro libQtDBus libQtCore and libQtGui.
It has been lately addressed in the newest release of opencv-python. It is not a fix to the source code, rather the fix is to force pip to compile the newly available source via
pip install --no-binary opencv-python opencv-python
This will cause opencv-python to use the same libraries as the host, so the conflict no longer exists.
According to this issue posted on the OpenCV GitHub, this is a known issue that the developer states is damn near impossible to fix. It is apparently caused by a conflict in any Qt installations on the system with the Qt that is shipped with OpenCV. There are some suggestions floating around to remove the libqt5x11extras5 package from the system. This may fix it for some but anyone running these libraries on a Linux distribution that uses a window manager based on Qt will render their desktop environment unusable by removing this package (having tried it myself).
You can try building OpenCV from source using the WITH_GTK=ON option when running cmake which will use GTK instead of Qt, circumventing the conflict. However, this is hard to make use of in Python when using virtual environments.
I haven't spent the time to fully appreciate this problem, but as I understand this is caused by multiple conflicting versions of some plugin in the environment. I tried installing building opencv-python but there were errors with that approach. Another suggestion is to change your import order, but I've had mixed success with that, and I couldn't get it to work on a project today.
But I found a workaround that worked for me. Install opencv-python-headless instead of opencv-python. This will avoid installing the conflicting plugins. It may not work for you depending on what features of opencv you need.
$ pip uninstall opencv-python
$ pip install opencv-python-headless
The error was fixed on my system, by simply updating one library.
To find out where it is coming from, assuming Linux, try the following,
LD_DEBUG=files python -c "import cv2"
or,
LD_DEBUG=files python -c "import cv2 ; img = cv2.imread('myimage.png',0) ; cv2.imshow('image',img) ; cv2.waitKey(0)"
On my machine, it failed in one of the blas libraries. I updated that library and the code now runs without error.
This is an old bug you can find it discussed in a number of online communities.
My test code is as follows. Notably the error has not reoccurred, and apparently has nothing to do with Qt.
import cv2
img = cv2.imread('sudoku.png',0)
cv2.imshow('image',img)
cv2.waitKey(0)
To me, the solution to this problem was removing Anaconda, then installing pip followed by installing OpenCV with a simple pip install command.
Cheerio,
I am trying to use Assimulo 2.9. on a Mac OS X. For that I downloaded and installed sundials via cmake by creating a builddir to the Download file and ../Downloads/sundials-2.7.0 running
$cmake ../Downloads/sundials-2.7.0
$make
$make install
This should install everything in /usr/local.
It gives me no error warning when doing this. But when I am trying to use assimulo in python, following error message occurs:
from .sundials import IDA, CVode
ImportError: No module named sundials
Any suggestions?
Thank you very much.
The trick was to install everything through homebrew and get the missing sundials.so file. It seems that the current assimulo-2.9 distribution on pypi does not provide this shared object library and therefore triggers this error message.
I got the same error, in Anaconda(Ubuntu 18.04). I installed pyfmi first, and then installed the dependencies (assimulo, sundials) according to the error message. After everything was installed, the pyfmi was not working by running an fmu example.
But i uninstalled all the related software. Then i reinstalled everything with certain order. I found the order of installation matters, which are: sundials --> assimulo --> pyfmi.
Everything is good now.