Your installed python is incomplete

InTime

How to fix “Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError.”?

9219 views October 26, 2020 June 4, 2021 pohheng 0

Symptom:

When running InTime in Linux, you encounter an error message containing:

“Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError.”

This may be due to the fact that the lzma library is not installed / detected properly.

Resolution:

(Ubuntu) Install the lzma library.

[root@host ~]# apt install liblzma-dev [root@host ~]# cd /lib/x86_64-linux-gnu

Create a symbolic link to the liblzma library file.

[root@host x86_64-linux-gnu]# ln -s liblzma.so.5 liblzma.so.0

(Note: The liblzma library file may be named differently on your system, but the symbolic link must be named liblzma.so.0)

(CentOS/RHEL) Install the lzma library.

[root@host ~]# yum install xz-libs

(SUSE) Install the lzma library.

[root@host ~]# zypper install lzma

Create a symbolic link to the liblzma library file to bin6 folder of InTime installation directory.

[root@host ~]# cd /bin6 [root@host bin6]$ ln -s /usr/lib64/liblzma.so.5 liblzma.so.0

Applies to:

Knowledge Base ID: 202008202 — Last Review: Jan 01 2021 — Revision: 1.0

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Problem with lzma module #28219

Problem with lzma module #28219

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/usr/local/lib/python3.7/site-packages/pandas/compat/__init__.py:84: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError.

I get this error when I run the code and I don’t know how to fix it

The text was updated successfully, but these errors were encountered:

That’s just a warning, not an error.

You’ll need to reinstall Python. If you’re building from source you need to make sure that the proper headers are in place.

I’ve installed python again but same error

I had this problem recently . but here, upgrading from Python 3.7.3 to Python 3.7.4 solved the problem!

@Anatras another user mentioned the xz library.

Closing, since this is an issue with the Python install, not pandas.

When you’re getting above warning and building Python from source, make sure to

• Include required packages. Here, install the lzma module sudo apt-get install liblzma-dev
• Rebuild from source directory configure && make and sudo make install

These steps removed the warning for my Python 3.7.3.
See also this Stack Overflow question

Me upgrading 3.7.2 to 2.7.6 solved the problem.

I was getting this warning:
/Users/usr/.pyenv/versions/3.9.5/lib/python3.9/site-packages/pandas/compat/__init__.py:97: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError.

I was finally able to get rid of it with this command:
CPPFLAGS=»-I$(brew —prefix xz)/include» pyenv install [your version]

Just thought I’d drop this here for anyone with my same problem.

OS: Big Sur
M1 chip
pyenv
python 3.9.5

OS: Monterey
M1 chip
pyenv
python 3.9.7

thank @corbinday its work in python 3.9.6

@corbinday ‘s solution works: CPPFLAGS=»-I$(brew —prefix xz)/include» pyenv install 3.10.0

OS: Monterey
M1 chip
pyenv
python 3.10.0

i tried @corbinday solution.. didn’t work for me.

OS: Monterey
M1 chip
pyenv (installed via homebrew)
python 3.10.0

Then i create a venv using that and then when i run pandas

/Users/kimsia/.venv/data-engineer-py3100/lib/python3.10/site-packages/pandas/compat/__init__.py:124: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError. warnings.warn(msg) 

UPDATE 2022-01-13 18:11 (SOLVED)

The issue is sovled when i

and then repeat the same thing because now 3.10.1 is now available

CFLAGS="-I$(brew --prefix xz)/include" LDFLAGS="-L$(brew --prefix xz)/lib" pyenv install 3.10.1 

/Users/kimsia/.pyenv/versions/3.10.1/bin/python3.10 -m venv ~/.venv/data-engineer-py3101 

activate the venv then reinstall the pandas and then proceed with my use case and now the lzma warning is gone

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BUG: UserWarning: Could not import the lzma module. Your installed Python is incomplete. #35844

BUG: UserWarning: Could not import the lzma module. Your installed Python is incomplete. #35844

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• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of pandas.

Note: Please read this guide detailing how to provide the necessary information for us to reproduce your bug.

Code Sample, a copy-pastable example

import pandas as pd file = 'financial.csv' df = pd.read_csv(file) df.head(10)

Problem description

A simple csv import like the one above produce a user warning which arose since I had to move the HomeBrew directory into a custom location due to IT settings not letting me write anymore on the /usr/local.

I have since then reinstalled a fresh version of all the packages via pip as well as the zx module via homebrew.

Accordingly to this user, he was able to resolve by adding the following command into the .zshrc

export LDFLAGS=»-L$HOME/homebrew/opt/xz/lib $LDFLAGS»
export CPPFLAGS=»-I$HOME/homebrew/opt/xz/include $CPPFLAGS»
export PKG_CONFIG_PATH=»$HOME/homebrew/opt/xz/lib/pkgconfig $PKG_CONFIG_PATH»

Expected Output

Output of pd.show_versions()

INSTALLED VERSIONS

commit : f2ca0a2
python : 3.8.5.final.0
python-bits : 64
OS : Darwin
OS-release : 19.6.0
Version : Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
machine : x86_64
processor : i386
byteorder : little
LC_ALL : None
LANG : en_GB.UTF-8
LOCALE : en_GB.UTF-8

pandas : 1.1.1
numpy : 1.19.1
pytz : 2020.1
dateutil : 2.8.1
pip : 20.2.2
setuptools : 47.1.0
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : 1.3.3
lxml.etree : None
html5lib : 1.1
pymysql : None
psycopg2 : None
jinja2 : 2.11.2
IPython : 7.17.0
pandas_datareader: None
bs4 : None
bottleneck : None
fsspec : None
fastparquet : None
gcsfs : None
matplotlib : 3.3.1
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : None
pytables : None
pyxlsb : 1.0.6
s3fs : None
scipy : 1.5.2
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
xlwt : None
numba : None

The text was updated successfully, but these errors were encountered:

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UserWarning: Could not import the lzma module. Your installed Python is incomplete

If you compile Python from source, you must have the lzma-dev package installed, or it will not be built into python.

For ubuntu: sudo apt-get install liblzma-dev

For centos: yum install -y xz-devel

Then configure && make && make install

Solution 2

I used other good answers from here and didn’t solve the problem (Ubuntu 18.04, Python3.8), still get this warning. Actually there is one more package is needed to be installed to solve the problem:

So the whole pipeline (run in the python source code folder):

sudo apt-get install liblzma-dev sudo apt-get install lzma ./configure --enable-optimizations sudo make sudo make altinstall 

Solution 3

On MacOS and pyenv (https://realpython.com/intro-to-pyenv/), I was able to have this warning go away by having xz installed with homebrew. Using version python 3.6.9 as an example

brew install xz && pyenv install 3.6.9

To use installed python, one needs to add this into .bash_profile

and start using it by running

Solution 4

On macOS, if you manage your python with pyenv and package with homebrew, you need to install «xz» first:

After installing xz, you can install python 3.8 by (I’m using 3.8.2 as an example:

Above will fix the problem.

Solution 5

If you are using centos and compile python from source, you can install from following commands

For centos: sudo yum install -y xz-devel

Recompile python from source code

cd Python-3.8*/ ./configure --enable-optimizations sudo make altinstall 

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After Installing Google Cloud Bigquery Module, if I import the module into python code. I see this warning message. Happening to me in python 3.7.3 Virtualenv. Tried to reinstall GCP bigquery module Expectation-in python code if we write» from google.cloud import bigquery «.Should not result in any error or messege.

import os import sys import logging from datetime import datetime from google.cloud import bigquery 

/home/informatica/.local/lib/python3.7/site-packages/pandas/compat/__init__.py:84: UserWarning: Could not import the lzma module. Your installed Python is incomplete. Attempting to use lzma compression will result in a RuntimeError. warnings.warn(msg) exit() 

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