ImportError: `GLIBCXX_3.4.30' not found #1282

rvanlaar · 2022-09-22T19:53:55Z

Running

import scipy.stats as stats

gives the following error:

ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/handboek/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-38-x86_64-linux-gnu.so)

It might be a path issue. The created miniconda enviroment by reticulate is sound.
And the included libstdc++.so.6 in the miniconda enviroment does contain the GLIBCXX_3_4.30 string.

/home/handboek/.local/share/r-miniconda/envs/r-reticulate/bin/python
Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18) 
[GCC 10.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scipy.stats as stats
>>>

reproduction:

> library("reticulate")
> install_miniconda()
< snip>
> py_discover_config()
python:         /home/handboek/.local/share/r-miniconda/envs/r-reticulate/bin/python
libpython:      /home/handboek/.local/share/r-miniconda/envs/r-reticulate/lib/libpython3.8.so
pythonhome:     /home/handboek/.local/share/r-miniconda/envs/r-reticulate:/home/handboek/.local/share/r-miniconda/envs/r-reticulate
version:        3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18)  [GCC 10.3.0]
numpy:          /home/handboek/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/numpy
numpy_version:  1.23.3
> pad <- py_discover_config()
> use_python(pad$python)
> py_install("scipy")
+ '/home/handboek/.local/share/r-miniconda/bin/conda' 'install' '--yes' '--prefix' '/home/handboek/.local/share/r-miniconda/envs/r-reticulate' '-c' 'conda-forge' 'scipy'
Collecting package metadata (current_repodata.json): done
Solving environment: done
<snip>
Downloading and Extracting Packages
scipy-1.9.1          | 26.2 MB   | ################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Retrieving notices: ...working... done
> repl_python()
Python 3.8.13 (/home/handboek/.local/share/r-miniconda/envs/r-reticulate/bin/python)
Reticulate 1.26 REPL -- A Python interpreter in R.
Enter 'exit' or 'quit' to exit the REPL and return to R.
>>> import scipy.stats as stats
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/handboek/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/scipy/optimize/_highs/_highs_wrapper.cpython-38-x86_64-linux-gnu.so)
>>> exit

environment

> utils::sessionInfo() 
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reticulate_1.26

loaded via a namespace (and not attached):
 [1] compiler_4.2.1  here_1.0.1      Matrix_1.5-1    rprojroot_2.0.3
 [5] rappdirs_0.3.3  Rcpp_1.0.9      grid_4.2.1      jsonlite_1.8.0 
 [9] png_0.1-7       lattice_0.20-45

> reticulate::py_config() 
python:         /home/handboek/.local/share/r-miniconda/envs/r-reticulate/bin/python
libpython:      /home/handboek/.local/share/r-miniconda/envs/r-reticulate/lib/libpython3.8.so
pythonhome:     /home/handboek/.local/share/r-miniconda/envs/r-reticulate:/home/handboek/.local/share/r-miniconda/envs/r-reticulate
version:        3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:18)  [GCC 10.3.0]
numpy:          /home/handboek/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/numpy
numpy_version:  1.23.3
sys:            [builtin module]

NOTE: Python version was forced by use_python function

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

yoshidk6 · 2022-10-09T07:03:58Z

I ran into a similar situation when I was trying to import xgboost in R with reticulate, while xgboost import was perfectly fine in Python REPL.
The solution that worked for me was downgrading xgboost from 1.6.x (which requires GLIBCXX_3.4.30) to 1.5.x.

TL;DR

The problem seems to be stemming from different libstdc++.so.6 being called between R (& reticulate) and Conda/Python. (Note for those who are not familiar including myself: this post (https://unix.stackexchange.com/a/557929) had nice explanations on what exactly are libstdc++.so.6, GLIBCXX_*, ...)

In your case /usr/lib/x86_64-linux-gnu/libstdc++.so.6, which I assume is the system default, is used by R & reticulate.
If you run strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX, you will see up to which version of GLIBCXX your libstdc++.so.6 supports.
In my case it was up to GLIBCXX_3.4.28 and did not include GLIBCXX_3.4.30. This was the cause of the issue.

As far as I can see, there are couple of potential solutions. Only the last one worked for me.

Upgrade your system default libstd (libstdc++.so.6: version `GLIBCXX_3.4.22' not found lhelontra/tensorflow-on-arm#13 (comment)). I didn't have sudo access
Set LD_LIBRARY_PATH to tell R which exact library to use. This might not work according to this comment (`GLIBCXX_3.4.21' not found #841 (comment))
Replace the system default libstdc++.so.6 with symbolic link to a newer version of libstdc++.so.6 somewhere in your system, like the one in conda (`GLIBCXX_3.4.21' not found #841 (comment)). Again I didn't have sudo access
Use an older version of Python packages that depends only on an older version of GLIBCXX

It would be super nice if reticulate package can detect this kind of incompatibility and flag this in a warning message.

MKhGenesis · 2022-11-08T20:03:35Z

https://stackoverflow.com/questions/73317676/importerror-usr-lib-aarch64-linux-gnu-libstdc-so-6-version-glibcxx-3-4-30
try this one

ArnoZWang · 2023-01-15T16:49:06Z

https://stackoverflow.com/questions/58424974/anaconda-importerror-usr-lib64-libstdc-so-6-version-glibcxx-3-4-21-not-fo
Have you ever tried this solution? It worked fine for me.

HeyWeCome · 2023-11-01T03:03:33Z

执行这个命令就可以了：

conda install -c conda-forge gcc=12.1.0

t-kalinowski · 2023-11-01T13:23:12Z

This is due to a binary incompatibility between conda and the R installation.

The most straightforward solution is to switch from conda to virtual environments, which don't suffer from the same problem.

library(reticulate)
install_python("3.10:latest")
virtualenv_create("r-scipy", version = "3.10", packages = "scipy")

(( The less straightforward solution is to have conda provide the R binary and all R packages. Note that this approach means that you can't use pre-built packages from CRAN or RStudio builds provided by Posit. ))

- add support for importing modules from various locations - R CMD Check and tests are passing - Note: Metworx does not support "pandas" via a conda environment. It seems to stem from different libstdc++.so.6 versions being called between R and conda/python. A virtual environment may not have this issue, but using the pre-set path to python avoids this issue within conda environments. See more details here: rstudio/reticulate#1282

mailmrcai · 2023-12-07T03:21:17Z

this command is ok: conda install -c conda-forge gcc=12.1.0

avishai987 · 2024-04-01T10:40:08Z

I also recommend to switch to virtual env, that's the only solution that solved the 'GLIBCXX_3.4.30' not found error
(I also don't have sudo premission).

library(reticulate)
virtualenv_create("<your_path>/cnmf_dev", packages = <your_packages>,required = T)
use_virtualenv("<your_path>/cnmf_dev",required = T)

LukeLIN-web · 2024-04-09T10:34:42Z

this command is ok: conda install -c conda-forge gcc=12.1.0

Solving environment: unsuccessful initial attempt using frozen solve. Retrying with flexible solve.

I tried export LD_LIBRARY_PATH=$LD_LIBRARY_PATH: $HOME/miniconda3/lib/ it also failed.

Finally, I find the solution
pybind/pybind11#3453 (comment)

It can works.

lumbric · 2024-04-29T09:23:47Z

This issue is not specific to reticulate. I've written a comprehensive overview on stackoverflow explaining what is happening here and possible ways to fix it.

WT215 · 2024-09-04T12:38:23Z

I also recommend to switch to virtual env, that's the only solution that solved the 'GLIBCXX_3.4.30' not found error (I also don't have sudo premission).
library(reticulate)
virtualenv_create("<your_path>/cnmf_dev", packages = <your_packages>,required = T)
use_virtualenv("<your_path>/cnmf_dev",required = T)

I think this is the most robust way, particularly when you are working on a server.

yoshidk6 mentioned this issue Oct 9, 2022

`GLIBCXX_3.4.21' not found #841

Open

t-kalinowski added the conda label Jan 6, 2023

fabianschenk mentioned this issue Apr 27, 2023

Virtual envs: ImportError with bin/opensfm_run_all mapillary/OpenSfM#989

Open

5 tasks

FdyCN mentioned this issue Jul 25, 2023

关于导入from fastllm_pytools import llm 报.so库的问题 ztxz16/fastllm#102

Closed

Cohee1207 mentioned this issue Sep 5, 2023

Error: Could not import the 'talkinghead' module. SillyTavern/SillyTavern-Extras#148

Open

t-kalinowski closed this as completed Nov 1, 2023

drprojects mentioned this issue Apr 29, 2024

Install script makes seemingly incorrect assumptions about PGEOF's environment drprojects/superpoint_transformer#102

Closed

oneThousand1000 mentioned this issue Jun 4, 2024

OSError: ("/home/jeonguk/miniconda3/envs/text_to_3dportrait/bin/../lib/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /lib/x86_64-linux-gnu/libLLVM-15.so.1)", 'libOSMesa.so.8', 'libOSMesa.so.8') oneThousand1000/Portrait3D#6

Closed

abhihjoshi mentioned this issue Jul 19, 2024

Numpy 1.26 not finding GLIBCXX_3.4.30 numpy/numpy#26986

Closed

t-kalinowski mentioned this issue Sep 19, 2024

Automatically Set Up Python Environments for R Packages #1671

Open

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ImportError: `GLIBCXX_3.4.30' not found #1282

ImportError: `GLIBCXX_3.4.30' not found #1282

rvanlaar commented Sep 22, 2022 •

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yoshidk6 commented Oct 9, 2022 •

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MKhGenesis commented Nov 8, 2022

ArnoZWang commented Jan 15, 2023

HeyWeCome commented Nov 1, 2023

t-kalinowski commented Nov 1, 2023

mailmrcai commented Dec 7, 2023

avishai987 commented Apr 1, 2024

LukeLIN-web commented Apr 9, 2024 •

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lumbric commented Apr 29, 2024

WT215 commented Sep 4, 2024

ImportError: `GLIBCXX_3.4.30' not found #1282

ImportError: `GLIBCXX_3.4.30' not found #1282

Comments

rvanlaar commented Sep 22, 2022 • edited Loading

reproduction:

environment

yoshidk6 commented Oct 9, 2022 • edited Loading

TL;DR

MKhGenesis commented Nov 8, 2022

ArnoZWang commented Jan 15, 2023

HeyWeCome commented Nov 1, 2023

t-kalinowski commented Nov 1, 2023

mailmrcai commented Dec 7, 2023

avishai987 commented Apr 1, 2024

LukeLIN-web commented Apr 9, 2024 • edited Loading

lumbric commented Apr 29, 2024

WT215 commented Sep 4, 2024

rvanlaar commented Sep 22, 2022 •

edited

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yoshidk6 commented Oct 9, 2022 •

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LukeLIN-web commented Apr 9, 2024 •

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