Could you please help me? 2 weeks ago I did brew upgrade and that somehow broke some dependencies in my Python project (I think that was the cause as it was compiling before) and I cannot seem to import scipy any more. The error message I am struggling with is the following:
ImportError: dlopen(/Users/albydeca/indProjSource/venv/lib/python2.7/site-packages/scipy/optimize/minpack2.so, 2):
Library not loaded: /usr/local/lib/gcc/x86_64-apple-darwin14.0.0/4.9.2/libgfortran.3.dylib
Referenced from:/Users/albydeca/indProjSource/venv/lib/python2.7/site-packages/scipy/optimize/minpack2.so
Reason: image not found
Triggered from :
File "/Users/albydeca/indProjSource/venv/lib/python2.7/site- packages/scipy/optimize/linesearch.py", line 18, in <module>
from scipy.optimize import minpack2
This is due to the fact that my path is as follows:
/usr/local/lib/gcc/x86_64-apple-darwin13.1.0/4.7.3
and fortran.3.dylib is not there
I have tried searching how I can get that folder but brew installing gcc49 does not do the job. My gcc choices are either 5 or x86_64-apple-darwin13.1.0
Have you encountered this or similar messages before? Do you know how I can fix this?
Thanks in advance
I know how to avoid this problem. Get a Python Distribution that has scipy included already. It's called Anaconda from https://www.continuum.io/downloads
To avoid this problem in the future is stop messing with your main environment by instead using virtualenv's or conda environments.
Related
I am running Eclipse IDE 4.20.0 with a PyDev Interpreter on Windows10. I am trying try to get [Camelot][1] to run within my script but continue to get the error-
"Original error was: No module named 'numpy.core._multiarray_umath'"
For each, I have used pip install to install camelot, tabula-py, numpy, pandas, etc. and all of them seemed to install appropriately. My Eclipse Project Properties PYTHONPATH is pointed to the install location and I haven't had issues with other libraries I have installed previously.
The Python version is: Python3.7
The NumPy version is: "1.21.5"
I also tried reverting numpy to an older version (1.15.1) but had no success there based on other posts that I have seen here on stackoverflow. Additionally, I have read the numpy support site that is listed in the error below but can't find anything that would be of note in my system as an issue...
Ultimately, I am attempting to read tables from a PDF in python but it seems that the libraries available (camelot, tabula, etc.) all give me the same issue with numpy. Any suggestions here would be greatly appreciated.
The full error that I am getting is -
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed.
This error can happen for many reasons, often due to issues with your setup or how NumPy was installed.
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
The Python version is: Python3.7 from "C:\Users~~~\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\python.exe"
The NumPy version is: "1.21.5"
and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.
Original error was: No module named 'numpy.core._multiarray_umath'
I recently updated Anaconda (Spyder (Python 3.6), Windows 10). Several of my libaries disappeared and had to be re-installed. However, I have been unable to reinstall scipy. When I run "conda install scipy -f" from the Windows PowerShell, scipy seems to be reinstalled. However even if I close Spyder and restat Windows, I continue to get the error: ModuleNotFoundError: No module named 'scipy'.
I know that problems similar to this one have been posted previously, but I have been unable to find anything that seems to fix the problems.
Thanks in advance for any advice (and apologies if this question was posted yesterday as well).
I battled with this same issue. The reason is most likely because you already have a file in the current directory called scipy.py. For example, when I first started with scipy, i made a file literally called scipy.py to practice in. Then, when I tried to import scipy from a different file, the first instance of 'scipy.py' was my practice folder, rather than the actual package which was further into the directory.
I advise you check for folders that you may have named scipy.py that aren't the actual scipy package. I could be wrong, but it seems likely that python will first search the folder it saves your files to, and then trundle over to the packages folder saved elsewhere.
Hopefully this helps some other folks who are stumped by the same issue!
I am trying to install a software called p4vasp:
https://github.com/orest-d/p4vasp/blob/master/README.MacOS.
I am getting this error message:
You need to get version 2.0 (or later) of PyGTK for this to work. You can get source code from http://www.pygtk.org
So I go there and follow the steps, but when I try to run the python script hello.py it fails:
File "hello.py", line 1, in
import gi
ImportError: No module named gi.
I think this could the problem.
pygobject3 3.36.1 is already installed and gtk+3 3.24.22 as well.
I have tried all the solutions, none worked so far.. Could someone help me please?
Thank you in advance.
Best wishes to all
I'm using a remote machine for computation and data analysis. I don't have sudo access in this machine, for data analysis purposes I want to use python libraries such as vtk etc since pip is not installed in this machine, I set up a 'virtual-environment' and install VTK there,
I used the method explained here (https://stackoverflow.com/a/13958308/10755782). Then I could install vtk in the virtual environment using pip.
But now the problem is that I can't import matplotlib.pyplot, it is giving me the error
ImportError: No module named Tkinter.
This error is strange because matplotlib.pyplot works in this particular system outside my virtual-environment. There are a few workarounds to start using matplotlib.pyplot without tkinter such as this (https://stackoverflow.com/a/49988926/10755782), but this is not helpfull in my case as this machine is remote-accessed and I need 'tkinter' to view the graphs on my screen.
I tried installing 'tkinter' inside my virtual-env, but I could not ( since we can't install 'tkinter' with pip and I don't have sudo access).
As I could not find any immediate solution to this problem anywhere I tried to fix this myself and I did the following,
inside my virtual environment, the version of matplotlib was 2.2.4 and outside it was 1.2.0 ( which is working fine). So I downgraded the version of matplotlib inside my virtual environment to 1.2.0
pip install 'matplotlib==1.2.0' --force-reinstall
now I have the same version of matplotlib inside and outside the virtual env. But now, when I try import matplotlilb.pyplot as plt I'm getting the error
ImportError: /b/home/ipcms/rcheenik/Python_virt-env/python2.7/my_new_env/lib/python2.7/site-
packages/matplotlib/_cntr.so: undefined symbol: _intel_fast_memset
Is there any way to fix this ^^ error? any of these following will be able to help me.
without OR is there any way to install tkinter without sudo ? or inside the 'virtual-environment' ?
OR is there any alternatives to matplotlib.pyplot which works without 'tkinter' and still display graphs remotely? ( not favourable, as I have to rewrite the entire code )
Thanks in advance for the help.
I found this answer to a similar question however, which I believe would solve your issue.
https://stackoverflow.com/a/49988926/8775307
It imports matplotlib.pyplot without tkinter. I don't know if all the features are actually included though, so you'll have to test and let us know :).
You could always write to the administrator and request Tkinter - it's a widely used and useful package, so they might be willing to include it.
RDKit could be a nice package if it wasn't so complicated to install.
Here on SO, there are several questions having problems with the installation of RDKit.
However, on different operating systems or different environments.
My configuration is:
Win10, Python 3.7.4, pip is installed, PATH is set, PYTHONPATH is set.
The installation of other modules is working fine via python -m pip install <package>.
I'm aware that the site recommends the fastest installation with Anaconda.
However, I don't have and don't want Anaconda.
On the webpage it says:
"Get the appropriate windows binary build from: https://github.com/rdkit/rdkit/releases".
However, there are no binaries of the latest versions.
This means, I would have to build it from source. I'm hesitating because the process seems to be pretty complicated, many extra installations with new problems and unknowns, and furthermore, the instructions seem to be outdated and incomplete for somebody who would build binaries from the source for the first time.
So, then I tried some unofficial binaries of RDKit.
If I unpack them and set the paths according to instructions, I get this error message:
>>> from rdkit import Chem
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "C:\Users\xyz\Programs\RDKit\rdkit\__init__.py", line 2, in <module>
from .rdBase import rdkitVersion as __version__
ImportError: DLL load failed: The specified module could not be found.
So, finally my questions:
How to properly install RDKit with the above mentioned configuration?
What is the specified DLL which is missing?
Where is it expecting it and searching it?
Are these RDKit 3.6 binaries maybe incompatible with Python 3.7.4?
I'm pretty sure it is probably a "small" thing (a path here or a check there), but I'm stuck. Thank you for any hints.
Update:
Apparently, it is not just a "small" thing. Chances to get this to work are most likely very low.
In the meantime I found this:
https://github.com/rdkit/rdkit/issues/1812
https://github.com/rdkit/rdkit/issues/2389
If the author of rdkit writes (April 2019):
I would be happy to be able to do pip distributions of the RDKit, but
to the best of my knowledge no one has managed to figure out how to
make it actually work.
I'd be happy to accept a PR from someone who has figured this out, but
I am not likely to have the time to do this myself anytime in the near
future.
So, if anybody feels capable achieving this, please feel free.
I will invest time in something else or will have to switch to Anaconda if I want to use RDKit.
On the webpage you linked there is a section about missing DLLs:
"In Win7 systems, you may run into trouble due to missing DLLs, see one thread from the mailing list: http://www.mail-archive.com/rdkit-discuss#lists.sourceforge.net/msg01632.html You can download the missing DLLs from here: http://www.microsoft.com/en-us/download/details.aspx?id=5555"
Not sure if this helps