import("pandas") error - version `GLIBCXX_3.4.21' not found
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 30/100
Research direction
Start by reproducing the exact conda setup and import("pandas") call on CentOS 7. Read the rpytools/loader.py entry point shown in the traceback and inspect the reticulate paths involved in conda_create(), conda_install(), and use_condaenv(). Done means the reproducible example imports pandas without the GLIBCXX_3.4.21 error.
Written by the indexing model from the issue text.
Description
Reproducible example:
library(reticulate)
path_to_conda='~/bin/Software/miniconda3/bin/conda'
conda_create("test", conda=path_to_conda)
conda_install("test", c("pandas", "matplotlib"), conda=path_to_conda)
use_condaenv("test", required=TRUE, conda = path_to_conda)
import("pandas")
Error Message:
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/user/bin/Software/miniconda3/envs/test/lib/python3.9/site-packages/pandas/_libs/window/aggregations.cpython-39-x86_64-linux-gnu.so)
Detailed traceback:
File "/home/user/R/x86_64-pc-linux-gnu-library/4.0/reticulate/python/rpytools/loader.py", line 19, in _import_hook
module = _import(
File "/home/user/bin/Software/miniconda3/envs/test/lib/python3.9/site-packages/pandas/__init__.py", line 51, in <module>
from pandas.core.api import (
File "/home/user/R/x86_64-pc-linux-gnu-library/4.0/reticulate/python/rpytools/loader.py", line 19, in _import_hook
module = _import(
File "/home/user/bin/Software/miniconda3/envs/test/lib/python3.9/site-packages/pandas/core/api.py", line 31, in <module>
from pandas.core.groupby import Grouper, NamedAgg
File "/home/user/R/x86_64-pc-linux-gnu-library/4.0/reticulate/python/rpytools/loader.py", line 19, in _import_hook
Session Info:
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /opt/R-4.0.3/lib64/R/lib/libRblas.so
LAPACK: /opt/R-4.0.3/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reticulate_1.18
loaded via a namespace (and not attached):
[1] compiler_4.0.3 Matrix_1.2-18 tools_4.0.3 rappdirs_0.3.1
[5] Rcpp_1.0.5 grid_4.0.3 jsonlite_1.7.1 lattice_0.20-41
- Dominant language
- R
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- Merged PRs (30d)
- 4
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