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mac mecab dlopen: symbol not found in flat namespace error

I want to import MeCab and use it, but that error comes out repeatedly.
MeCab-python is well installed.
I've tried Brew install and so on, and it's still the same.
I'd appreciate it if you could help me if you knew the solution.

Hmm. On a fresh macOS 13.1 Ventura, I just did this:
Installed miniconda https://docs.conda.io/en/latest/miniconda.html#latest-miniconda-installer-links
conda create -n mecab-tutorial and answering questions
conda activate mecab-tutorial
conda install python ipython and saying 'yes'
python -m pip install mecab-python3 unidic-lite
Then I was able to run this script:
import MeCab
wakati = MeCab.Tagger("-Owakati")
wakati.parse("pythonが大好きです").split()
# ['python', 'が', '大好き', 'です']
Looking at the path in the error in the screenshot, it looks like you installed a global Python in /Library which I don't want to try because I very much prefer to keep my Python environments local, hence using Conda above to create a custom environment to install MeCab packages in to ensure no cross-contamination later.
There's no guarantee that this will work if you try it since the error you're seeing seems to be a compiler issue (Python is finding MeCab, just having trouble calling a C++ function inside the binary), but if possible, can you try the Conda approach above?

Reticulate can't install python packages

I'm trying to run the Seurat pipeline in RStudio (Windows 10 , which requires having the python library 'umap-learn' installed (Seurat walkthrough: https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html).
To install said library, I'm using the reticulate library in R in the following manner:
library(reticulate)
py_install(packages = 'umap-learn')
I'm getting the following error:
Error in conda_python(envname = envname, conda = conda) :
conda environment r-reticulate not found
I've tried just about everything I can think of:
Providing py_install with a path to python directly
Uninstall / Reinstall of RStudio
Uninstall / Reinstall of Anaconda
Tried adding Anaconda to system path
Using devtools version of Reticulate
Using the use_python function: use_python("C://Users/lvlah/Anaconda3/python.exe")
At my wit's end with this - none of my colleagues have had this issue. Any help would be appreciated.

I had the same problem and what seems to be an issue is that you need to first manually create the r-reticulate environment. I did it manually in Anaconda Navigator, but you can also do conda_create("r-reticulate") within R, as detailed in this tutorial.

I had exactly the same issue and after finding this helpful post I've solved it by installing OpenSSL. Hope it works for you!

conda skeleton cran uses wrong version of R

I am trying to package some R packages from CRAN to use in a conda environment because I am using a combination of Python and R packages for a bioinformatics pipeline. Because of other dependencies, I need to keep R at version 3.3
I made a brandnew environment with the version of Python and R I want:
$ conda create -n bioinfo python=3.6.3 r=3.3.2
There is no R installed in the root environment. Then I follow the instructions for conda skeleton:
(bioinfo)$ conda skeleton cran rootSolve
(bioinfo)$ conda skeleton cran rootSolve
(bioinfo)$ conda build r-rootsolve
For some reason, this keeps coming up with an R3.4 dependency, even though according to CRAN, the rootSolve package only needs R>=2.01! Where is this coming from??
The following NEW packages will be INSTALLED:
r-base: 3.4.2-haf99962_0
Though building the package does not actually change the version of R running in my environment, the package does not load. Any ideas, please?
R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
> library('rootSolve')
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/people/bioc1402/miniconda3/envs/bioinfo2/lib/R/library/rootSolve/libs/rootSolve.so':
/usr/people/bioc1402/miniconda3/envs/bioinfo2/lib/R/library/rootSolve/libs/rootSolve.so: undefined symbol: R_ExternalPtrAddrFn
In addition: Warning message:
package ‘rootSolve’ was built under R version 3.4.2
Error: package or namespace load failed for ‘rootSolve’

Apparently this was a bug, now fixed in conda-build 3.1.3,
https://github.com/conda/conda-build/issues/2562
Thanks conda team!
'conda build r-rootsolve --R=3.3.1' now works appropriately with the recipe generated by conda skeleton.

Installing gdal with conda and setting environmental variables

I have been trying to get the gdal library work using Python 2.7 and Anaconda in Windows 8 environment.
Besides gdal, I have also installed libgdal (frankly, I don't really understand the difference between the two). I now seem to have gdal 2.1.0 and 2.0.2 as well as libgdal 2.1.0.
However, when I run my Py code, there is a gdal error:
'gdalwarp' is not recognized as an internal or external command,
operable program or batch file.
I have already set the GDAL_DATA environmental variable to point to
C:\Anaconda\pkgs\libgdal-2.1.0-vc9_0\Library\share\gdal
I have also added a path, although I am not entirely sure where this should point to:
C:\Anaconda\pkgs\libgdal-2.1.0-vc9_0\Library\bin
I have tried the same with gdal 2.0.2 without success. gdalwarp.exe does seem to exist under libgdal 2.1.0 and gdal 2.0.2.
Any ideas? Is there an issue with the installation or have I not set the environmental variables correctly?
FYI, I have tried various installation commands, notably:
conda install gdal
conda install -c conda-forge gdal
conda install -c anaconda gdal
Addendum: I have found a manual solution: I set the GDAL_DATA and PATH variables in the terminal (pointing to libgdal 2.1.0) before running the code...
However, there is still an issue when I run my Py code: it is supposed to convert a tiff file to shp with gdal_polygonize:
cmd = 'gdal_polygonize.py %s -f "ESRI Shapefile" %s'%(dst_tif, dst_shp)
There is no error but the shapefile is not created (which leads to an error later on in the code). Any ideas as to why gdal is still not working correctly?
I have tried pointing the env variables to osgeo:
set PATH=%PATH%;C:\Anaconda2\Lib\site-packages\osgeo\scripts
set GDAL_DATA=C:\Anaconda2\Lib\site-packages\osgeo\data\gdal
Gdalinfo works but the gdal_polygonize used in my Py code does not appear to work.

The key is the activation script which is (potentially) executed when activating the environment. Not every GDAL build for Conda contains this. In my experience recent Conda-Forge builds are really good.
With your requirements of py27 and GDAL 2.1 i can get it working by following these steps:
1) Create a new environment: conda create -n gdaltest python=2.7
2) Activate: activate gdaltest
3) Install GDAL: conda install gdal=2.1 -c conda-forge
4) Reactivate environment: deactivate + activate gdaltest
This forces the just installed activation script to be executed, this sets the environment variables.
If i start python and run os.system("gdalinfo"), i can see its picked up correctly. And running os.environ['GDAL_DATA'] confirms the path is set correctly.
You can view the (de)activation script yourself at:
C:\Miniconda3\envs\<env name>\etc\conda\activate.d\gdal-activate.bat
A few years ago this didn't work as well as it does today, so make sure you have a recent Conda version (4.3.x) etc.
The benefit of this method is, that when switching environments, your paths are also changed accordingly. A "hard coded" GDAL_DATA path could potentially cause some compatibility issues if you mix and match different GDAL versions (although normally is should work OK).

Conda-build version not installed

C:\Users\%USER%>conda info
Current conda install:
platform : win-32
conda version : 3.16.0
conda-build version : not installed
python version : 2.7.10.final.0
requests version : 2.7.0
root environment : C:\Users\%USER%\Miniconda (writable)
default environment : C:\Users\%USER%\Miniconda
envs directories : C:\Users\%USER%\Miniconda\envs
package cache : C:\Users\%USER%\Miniconda\pkgs
channel URLs : https://repo.continuum.io/pkgs/free/win-32/
https://repo.continuum.io/pkgs/free/noarch/
https://repo.continuum.io/pkgs/pro/win-32/
https://repo.continuum.io/pkgs/pro/noarch/
config file : None
is foreign system : True
# NOTE:
# root directory 'C:\Users\%USER%\Miniconda' is uninitialized
I see my root directory is not initialized.
Additionally when I try to install a package (pandas eg) I get the following error:
C:\Users\%USER%>conda install pandas
Error: This installation of conda is not initialized. Use 'conda create -n
envname' to create a conda environment and 'source activate envname' to
activate it.
# Note that pip installing conda is not the recommended way for setting up your
# system. The recommended way for setting up a conda system is by installing
# Miniconda, see: http://repo.continuum.io/miniconda/index.html
I assume they are related but I am not sure the course of action.
I had anaconda/python27 up and running but wanted to update matplotlib and thought to reinstall python with conda to be "up to date".
The error is documented here, but to be honest I do not really get it.
I regret this as it is a bit tough to get up and running again!

I had a similar problem, but with Anaconda on Windows 8.1.
The python env variables are set from a previous python install.
The installer did not update (user)PYTHONHOME, (system)PYTHON_DIR, and (system)PYTHONPATH, so I manually set them to /Users/me/Anaconda/.
conda update conda
gave the error mentioned above. I added a new conda environment...
conda create -n notebook jupyter
activate notebook
which succeeded, but...
conda info --envs
...gives...
notebook C:\Users\<me>\Anaconda\envs\notebook
root * C:\Users\<me>\Anaconda
...and...
conda info
...
# NOTE: root directory 'C:\Users\me\Anaconda' is uninitialized.
I suspect that the installer failed due to the presence of the environment variables. I deleted the environment variables and the /Users/me/Anaconda directory, then installed miniconda.
All seems to be well now.
Note:
I had previously installed python at least three different ways.
{Chocolatey, Anaconda(all)[failed], python msi}