Description
Please answer these questions:
Does installing pymer4 into a clean conda environment in any of these
four ways solve the problem? If so, which worked and which didn't?
conda create --name test_env1 -c ejolly -c defaults -c conda-forge pymer4- Did not work
conda create --name test_env2 -c ejolly -c conda-forge -c defaults pymer4- Did not work
conda create --name test_env3 -c ejolly/label/pre-release -c defaults -c conda-forge pymer4- Did not work
conda create --name test_env4 -c ejolly/label/pre-release -c conda-forge -c defaults pymer4- Did not work
Please provide the following information
1. Description
After creating a Pymer4 Lmer model, it fails becuase of :
RRuntimeError: Error in initializePtr() :
function 'chm_factor_ldetL2' not provided by package 'Matrix'
active environment : pymer4
active env location : /Users/~/miniconda3/envs/pymer4
shell level : 4
user config file : /Users/~/.condarc
populated config files : /Users/~/.condarc
conda version : 24.1.2
conda-build version : not installed
python version : 3.11.7.final.0
solver : libmamba (default)
virtual packages : __archspec=1=m1
__conda=24.1.2=0
__osx=14.4=0
__unix=0=0
base environment : /Users/noah/miniconda3 (writable)
conda av data dir : /Users/noah/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/osx-arm64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/osx-arm64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/osx-arm64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /Users/~/miniconda3/pkgs
platform : osx-arm64
user-agent : conda/24.1.2 requests/2.31.0 CPython/3.11.7 Darwin/23.4.0 OSX/14.4 solver/libmamba conda-libmamba-
solver/23.12.0 libmambapy/1.5.3
UID:GID : 501:20
netrc file : None
offline mode : False
2. Minimal reproducible example
These are the shortest steps that reconstruct the problem.
-
the command or commands you ran to to install pymer4:
conda install pymer4 ... -
create --name pymer4 -c ejolly -c conda-forge -c defaults pymer4 spyder -
a Python code snippet, the shorter the better, that runs and exhibits the issue
I'm trying to fit a linear mixed effect model. I tried this in both jupyter lab and spyder, both were installed in the same line as conda create --name...., so they followed the same channel priority as the installation of pymer. I tried the following code:
from pymer4.models import Lmer
import pandas as pd
df = pd.read_pickle('df.pkl')
mod = Lmer('Width~ TreatCntrl*PrePost+(1|Trail)', data = df)
print(mod.fit())
In both cases, I get the following error:
RRuntimeError: Error in initializePtr() :
function 'chm_factor_ldetL2' not provided by package 'Matrix'
I presume this is coming from the r-matrix package which according to the conda environment is as follows:
r-matrix 1.6_5 r42hb447869_0 conda-forge
My only suspicion is that this relates to the fact that I'm using an M1 Mac. I saw that you have previously resolved an issue with the M1 and no arch - Issue #38 , but perhaps this is something new? Here is some information about the conda environment pymer4 is installed in.
3. Conda environment
Activate the conda environment that has pymer4 installed, run the
following command in a terminal window, and upload the pymer4_issue.txt file as
an attachment with your issue.
conda list --explicit > pymer4_issue.txt
4. System information
Please provide the specifics about your computer hardware architecture and
operating system version. For example:
- Mac OSX, in a terminal window
$ uname -mprsv
Darwin 23.4.0 Darwin Kernel Version 23.4.0: Wed Feb 21 21:44:06 PST 2024; root:xnu-10063.101.15~2/RELEASE_ARM64_T8103 arm64 arm
$ sw_vers
ProductName: macOS
ProductVersion: 14.4
BuildVersion: 23E214