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#1 2020-07-29 17:33:01

kalix
Member
Registered: 2020-03-06
Posts: 14

Python Error When Trying to Use Matlibplot or Pandas

Hello!

So before I report a bug to arch I wanted to post what was going on here first to see if you guys think I should report a bug.

I am taking a class.  In that class we had to plot a histogram/scatter plot.  I installed Matplotlib/Pandas with pip.  The code I was trying to run is:

#importing numpy and random
import numpy as np
import random
import matplotlib.pyplot as plt

# #create a random list of 10000 values with range 0 - 169861098 and print list
randomlist = random.sample(range(0,169861098),10000)
print(randomlist)

#create a data set to plot points on a scatter plot 

x = [4, 6, 6, 2, 1, 9, 5, 6, 3, 4, 7, 9, 7]
y = [67, 34, 12, 89, 46, 96, 13, 90, 56, 78, 23, 11, 12]

plt.scatter(x,y)
plt.show()


#create a histogram from 1-1000 200 values

values = random.sample(range(1,1000),200)

plt.hist(values)
plt.show()

Now the code fails when it starts to try to run matplotlib (plt).  I get the following error:

/usr/bin/python: symbol lookup error: /usr/lib/python3.8/site-packages/PyQt5/Qt/plugins/iconengines/../../lib/libQt5Svg.so.5: undefined symbol: _ZdlPvm, version Qt_5

So I got on freenode #python and asked the guys there for help and they had me setup a virtual environment to run the code in and when I used that environment the code worked.  They had me run the code a few different ways with pyqt5 and pyside2 in the venv and both worked fine in the venv.  When I am not in the venv the code fails with the error stated above.

So I am wondering if I should report this as a bug or is this something that anyone has heard of happening before?

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#2 2020-07-29 18:00:56

arch_jsb
Member
Registered: 2010-03-13
Posts: 13

Re: Python Error When Trying to Use Matlibplot or Pandas

Works simply here in python3.7...  don't have an upto date arch install to test those libraries though.

Last edited by arch_jsb (2020-07-29 18:02:52)


Arch linux; FreeBSD; no 3rd...

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#3 2020-07-29 18:46:57

schard
Member
From: Hannover
Registered: 2016-05-06
Posts: 875
Website

Re: Python Error When Trying to Use Matlibplot or Pandas

I just tested your code on my machine.
It does not cause any error here.
Is your system up-to-date?
Did you maybe install some packages using pip as root (which you should never do)?

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#4 2020-07-29 21:21:07

kalix
Member
Registered: 2020-03-06
Posts: 14

Re: Python Error When Trying to Use Matlibplot or Pandas

Thanks for the response guys!  I know you shouldn't install packages as root with pip.  I don't think I have.  Is there a way to check to see if I mistakenly might have?  And yes Arch is fully updated. 

Also, I remember them saying, run this code

print("matplotlib:", plt.__file__)

And when I run that code (not in the venv) I get:

matplotlib: /home/aether/.local/lib/python3.8/site-packages/matplotlib/pyplot.py

I remember them saying "there you go" and some other stuff I can't remember completely but does this give you guys any information that maybe helpful in solving this issue?  I am brand new to python and any help would be greatly appreciated!!

Last edited by kalix (2020-07-29 21:23:23)

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#5 2020-07-29 22:28:48

arch_jsb
Member
Registered: 2010-03-13
Posts: 13

Re: Python Error When Trying to Use Matlibplot or Pandas

show the output of
/usr/local/bin/python --version?

reinstall qt5-svg?

/edit/

that should be /usr/bin/python --version

Sorry!

Last edited by arch_jsb (2020-07-30 11:54:59)


Arch linux; FreeBSD; no 3rd...

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#6 2020-07-29 22:52:10

kalix
Member
Registered: 2020-03-06
Posts: 14

Re: Python Error When Trying to Use Matlibplot or Pandas

EDIT: Tried to reinstall qt5-svg and still the same error message.

So this is interesting. 

I ran that code and got:

bash: /usr/local/bin/python: No such file or directory

Seems like its not there... Oh and are ~/.local and /usr/local related ?

Also should i try to reinstall qt5-svg with pip ?

Thanks for the response.

Last edited by kalix (2020-07-30 00:00:55)

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#7 2020-07-30 00:50:36

eschwartz
Trusted User/Bug Wrangler
Registered: 2014-08-08
Posts: 3,534

Re: Python Error When Trying to Use Matlibplot or Pandas

kalix wrote:

I installed Matplotlib/Pandas with pip.

You can install it with

pacman -Si python-matplotlib python-pandas
kalix wrote:

Now the code fails when it starts to try to run matplotlib (plt).  I get the following error:

/usr/bin/python: symbol lookup error: /usr/lib/python3.8/site-packages/PyQt5/Qt/plugins/iconengines/../../lib/libQt5Svg.so.5: undefined symbol: _ZdlPvm, version Qt_5

Why is it trying to find the file /usr/lib/python3.8/site-packages/PyQt5/Qt/lib/libQt5Svg.so.5

This implies you're using some previously installed PyQt5 that was installed with sudo pip rather than pacman. Therein lies your problem. Install the "lostfiles" package, and run it to detect files which pacman doesn't know about. Any such files in /usr/lib/python3.8/site-packages/ are deeply suspicious, and probably caused by sudo pip. Therefore, delete them. tongue

kalix wrote:

So I got on freenode #python and asked the guys there for help and they had me setup a virtual environment to run the code in and when I used that environment the code worked.  They had me run the code a few different ways with pyqt5 and pyside2 in the venv and both worked fine in the venv.  When I am not in the venv the code fails with the error stated above.

So I am wondering if I should report this as a bug or is this something that anyone has heard of happening before?

When you set up a virtual environment, you reinstalled PyQt5 from PyPI, from scratch, using pip. That's why it worked. Because you had a broken outside the virtual environment.


Managing AUR repos The Right Way -- aurpublish (now a standalone tool)

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#8 2020-07-30 03:05:25

kalix
Member
Registered: 2020-03-06
Posts: 14

Re: Python Error When Trying to Use Matlibplot or Pandas

Awesome tool, so yeah among the ton of other files lostfiles came up with were:

/usr/lib/python3.8/site-packages/cv2
/usr/lib/python3.8/site-packages/cv2/cv2.cpython-38-x86_64-linux-gnu.so
/usr/lib/python3.8/site-packages/cv2/data
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_eye_tree_eyeglasses.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_eye.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_frontalcatface_extended.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_frontalcatface.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_frontalface_alt2.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_frontalface_alt_tree.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_frontalface_alt.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_frontalface_default.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_fullbody.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_lefteye_2splits.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_licence_plate_rus_16stages.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_lowerbody.xml
/usr/lib/python3.8/site-packages/cv2/data/haarcascade_profileface.xml
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/usr/lib/python3.8/site-packages/cv2/.libs/libQtCore-ada04e4a.so.4.8.7
/usr/lib/python3.8/site-packages/cv2/.libs/libQtGui-903938cd.so.4.8.7
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/usr/lib/python3.8/site-packages/PyQt5/uic/port_v2/as_string.py
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/usr/lib/python3.8/site-packages/PyQt5/uic/port_v2/__pycache__/as_string.cpython-38.pyc
/usr/lib/python3.8/site-packages/PyQt5/uic/port_v2/__pycache__/__init__.cpython-38.pyc
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/usr/lib/python3.8/site-packages/PyQt5/uic/port_v2/__pycache__/string_io.cpython-38.pyc
/usr/lib/python3.8/site-packages/PyQt5/uic/port_v2/string_io.py

So I think you are right.  My question is how do i fix this? 


Thanks again, awesome tool!

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#9 2020-07-30 12:16:44

V1del
Forum Moderator
Registered: 2012-10-16
Posts: 10,137

Re: Python Error When Trying to Use Matlibplot or Pandas

Delete them, install the relevant packages from the repos

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#10 2020-08-02 19:39:28

kalix
Member
Registered: 2020-03-06
Posts: 14

Re: Python Error When Trying to Use Matlibplot or Pandas

Alright so, I had a chance to remove those files and reinstall matplotlib with:

pacman -S python-matplotlib

Now when I try to run the code, I get:

 
python_numpy_assignment.py:18: UserWarning: Matplotlib is currently using agg, which is a non-GUI backend, so cannot show the figure.
plt.show()
 

From the research I did I have to install some qt5 (with a gui) variant of the package but I'm not sure what its called and kinda wanted to see if I could get some advice from you guys on what I should do to resolve this.


Again thank you for the help !

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#11 2020-08-02 20:03:33

eschwartz
Trusted User/Bug Wrangler
Registered: 2014-08-08
Posts: 3,534

Re: Python Error When Trying to Use Matlibplot or Pandas

https://matplotlib.org/faq/usage_faq.ht … -a-backend

Select your preferred backend in matplotlibrc.


Managing AUR repos The Right Way -- aurpublish (now a standalone tool)

Offline

#12 2020-08-03 02:25:24

kalix
Member
Registered: 2020-03-06
Posts: 14

Re: Python Error When Trying to Use Matlibplot or Pandas

Awesome thank you so much!!

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