Open-MSS
expat XML error after installation of MSS 9.2.0
After installation of MSS 9.2.0 (using miniforge and mamba) and starting the server, I got an error related to expat. Version 2.6.2 was of expat was installed.
I downgraded to version 2.6.1 which solved the issue.
I found similar reports here: https://github.com/matplotlib/matplotlib/issues/28235
The error log when starting the server looked as follows:
[Wed Aug 28 16:54:07.192427 2024] [wsgi:info] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] mod_wsgi (pid=1242726, process='MSS', application=''): Loading Python script file '/home/mss/summer23/wsgi/wms.wsgi'. [Wed Aug 28 16:54:07.333530 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] mod_wsgi (pid=1242726): Failed to exec Python script file '/home/mss/summer23/wsgi/wms.wsgi'. [Wed Aug 28 16:54:07.333583 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] mod_wsgi (pid=1242726): Exception occurred processing WSGI script '/home/mss/summer23/wsgi/wms.wsgi'. [Wed Aug 28 16:54:07.346490 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] Traceback (most recent call last): [Wed Aug 28 16:54:07.347016 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/summer23/wsgi/wms.wsgi", line 24, i n <module> [Wed Aug 28 16:54:07.347029 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from mslib.mswms.wms import app as application [Wed Aug 28 16:54:07.347040 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/mslib/mswms/wms.py", line 56, in <module> [Wed Aug 28 16:54:07.347056 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from chameleon import PageTemplateLoader [Wed Aug 28 16:54:07.347064 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/chameleon/__init__.py", line 1, in <module> [Wed Aug 28 16:54:07.347069 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from .zpt.template import PageTemplate [Wed Aug 28 16:54:07.347078 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/chameleon/zpt/template.py", line 17, in <module> [Wed Aug 28 16:54:07.347082 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from ..template import BaseTemplate [Wed Aug 28 16:54:07.347089 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/chameleon/template.py", line 48, in <module> [Wed Aug 28 16:54:07.347094 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from .loader import ModuleLoader [Wed Aug 28 16:54:07.347100 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/chameleon/loader.py", line 9, in <module> [Wed Aug 28 16:54:07.347105 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] import pkg_resources [Wed Aug 28 16:54:07.347128 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3. 11/site-packages/pkg_resources/__init__.py", line 63, in <module> [Wed Aug 28 16:54:07.347132 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] import plistlib [Wed Aug 28 16:54:07.347157 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3.11/plistlib.py", line 70, in <module> [Wed Aug 28 16:54:07.347162 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from xml.parsers.expat import ParserCreate [Wed Aug 28 16:54:07.347168 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] File "/home/mss/miniforge3/envs/mssenv/lib/python3.11/xml/parsers/expat.py", line 4, in <module> [Wed Aug 28 16:54:07.347189 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] from pyexpat import * [Wed Aug 28 16:54:07.347207 2024] [wsgi:error] [pid 1242726:tid 1242731] [remote 95.89.143.182:48816] ImportError: /home/mss/miniforge3/envs/mssenv/lib/python3.11/lib-dynload/pyexpat.cpython-311-x86_64-linux-gnu.so: undefined symbol: XML_SetReparseDeferralEnabled
on my develop system it looks like this, mod_wsgi is used on an apache setup.
Can you show a similar output on yours?
(mssenvtest2) reimarb@infinity:~$ mamba repoquery whoneeds expat
Executing the query expat
Name Version Build Depends Channel Subdir
───────────────────────────────────────────────────────────────────────────
dbus 1.13.6 h5008d03_3 expat >=2.4.2,<3.0a0 conda-forge linux-64
fontconfig 2.14.2 h14ed4e7_0 conda-forge linux-64
libexpat comes with python
mamba repoquery whoneeds libexpat
Executing the query libexpat
Name Version Build Depends Channel Subdir
──────────────────────────────────────────────────────────────────────────────────
python 3.11.6 hab00c5b_0_cpython libexpat >=2.5.0,<3.0a0 conda-forge linux-64
(mssenv) mss@forecast:~$ mamba repoquery whoneeds expat
Executing the query expat
Name Version Build Depends Channel Subdir
───────────────────────────────────────────────────────────────────────────
dbus 1.13.6 h5008d03_3 expat >=2.4.2,<3.0a0 conda-forge linux-64
fontconfig 2.14.2 h14ed4e7_0 conda-forge linux-64
(mssenv) mss@forecast:~$ mamba repoquery whoneeds libexpat
Executing the query libexpat
Name Version Build Depends Channel Subdir
──────────────────────────────────────────────────────────────────────────────────────────────
expat 2.6.1 h59595ed_0 libexpat 2.6.1 h59595ed_0 conda-forge linux-64
git 2.44.0 pl5321h709897a_0 conda-forge linux-64
gst-plugins-base 1.22.9 h8e1006c_0 conda-forge linux-64
python 3.11.8 hab00c5b_0_cpython conda-forge linux-64
qt-main 5.15.8 h5810be5_19 conda-forge linux-64
qt-webengine 5.15.8 h7517aa4_5 conda-forge linux-64
That is how it looks on my system.
Please can you verify when you update python to 3.11.9 (latest version) and latest version of expat that the problem exists
mamba install python==3.11.9 mamba install expat==2.6.2
and I need conda info for the report on the python-feedstock. https://github.com/conda-forge/python-feedstock/issues/701
This might be also related https://github.com/conda-forge/python-feedstock/issues/673
and I need
conda infofor the report on the python-feedstock. conda-forge/python-feedstock#701
(mssenv) mss@forecast:~$ conda info
active environment : mssenv
active env location : /home/mss/miniforge3/envs/mssenv
shell level : 2
user config file : /home/mss/.condarc
populated config files : /home/mss/miniforge3/.condarc
/home/mss/.condarc
conda version : 24.3.0
conda-build version : not installed
python version : 3.10.14.final.0
solver : libmamba (default)
virtual packages : __archspec=1=broadwell
__conda=24.3.0=0
__glibc=2.31=0
__linux=5.10.0=0
__unix=0=0
base environment : /home/mss/miniforge3 (writable)
conda av data dir : /home/mss/miniforge3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/mss/miniforge3/pkgs
/home/mss/.conda/pkgs
envs directories : /home/mss/miniforge3/envs
/home/mss/.conda/envs
platform : linux-64
user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/5.10.0-32-amd64 debian/11.10 glibc/2.31 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
UID:GID : 1000:1000
netrc file : None
offline mode : False
mamba install python==3.11.9 mamba install expat==2.6.2
Yeah, problem is persistent, changed back to python 3.11.8 and expat 2.6.1 ...
somehow the conda info seems to have a python version : 3.10.14.final.0
Did you done that differently?
somehow the conda info seems to have a
python version : 3.10.14.final.0Did you done that differently?
(base) mss@forecast:~$ conda info
active environment : base
active env location : /home/mss/miniforge3
shell level : 1
user config file : /home/mss/.condarc
populated config files : /home/mss/miniforge3/.condarc
/home/mss/.condarc
conda version : 24.3.0
conda-build version : not installed
python version : 3.10.14.final.0
solver : libmamba (default)
virtual packages : __archspec=1=broadwell
__conda=24.3.0=0
__glibc=2.31=0
__linux=5.10.0=0
__unix=0=0
base environment : /home/mss/miniforge3 (writable)
conda av data dir : /home/mss/miniforge3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/mss/miniforge3/pkgs
/home/mss/.conda/pkgs
envs directories : /home/mss/miniforge3/envs
/home/mss/.conda/envs
platform : linux-64
user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/5.10.0-32-amd64 debian/11.10 glibc/2.31 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
UID:GID : 1000:1000
netrc file : None
offline mode : False
(base) mss@forecast:~$ python --version
Python 3.10.14
(base) mss@forecast:~$ mamba activate mssenv
(mssenv) mss@forecast:~$ python --version
Python 3.11.8
(mssenv) mss@forecast:~$ conda info
active environment : mssenv
active env location : /home/mss/miniforge3/envs/mssenv
shell level : 2
user config file : /home/mss/.condarc
populated config files : /home/mss/miniforge3/.condarc
/home/mss/.condarc
conda version : 24.3.0
conda-build version : not installed
python version : 3.10.14.final.0
solver : libmamba (default)
virtual packages : __archspec=1=broadwell
__conda=24.3.0=0
__glibc=2.31=0
__linux=5.10.0=0
__unix=0=0
base environment : /home/mss/miniforge3 (writable)
conda av data dir : /home/mss/miniforge3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/mss/miniforge3/pkgs
/home/mss/.conda/pkgs
envs directories : /home/mss/miniforge3/envs
/home/mss/.conda/envs
platform : linux-64
user-agent : conda/24.3.0 requests/2.31.0 CPython/3.10.14 Linux/5.10.0-32-amd64 debian/11.10 glibc/2.31 solver/libmamba conda-libmamba-solver/24.1.0 libmambapy/1.5.8
UID:GID : 1000:1000
netrc file : None
offline mode : False
So it seems that conda info puts out the python version of the base installation, independent of the environment. But as you can see, in the environment python --version results in the correct version.