reticulate::import() gives error where direct python repl works fine

[leungi]

Issue, system and session info below.

Tried it with Python 3.5, 3.6 and 2.7, with same outcome.

Issue

[leungi@ohylpyt1-d /bin]$ R

R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
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Platform: x86_64-redhat-linux-gnu (64-bit)

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> reticulate::use_python("/home/leungi/miniconda3/envs/stooip-27/bin")
> reticulate::py_config()
python:         /home/leungi/miniconda3/envs/stooip-27/bin/python
libpython:      /home/leungi/miniconda3/envs/stooip-27/lib/libpython2.7.so
pythonhome:     /home/leungi/miniconda3/envs/stooip-27:/home/leungi/miniconda3/envs/stooip-27
version:        2.7.16 |Anaconda, Inc.| (default, Sep 24 2019, 21:51:30)  [GCC 7.3.0]
numpy:          /home/leungi/miniconda3/envs/stooip-27/lib/python2.7/site-packages/numpy
numpy_version:  1.16.5

python versions found:
 /home/leungi/miniconda3/envs/stooip-27/bin/python
 /bin/python
 /usr/bin/python
 /home/leungi/miniconda3/envs/py35/bin/python
 /home/leungi/miniconda3/envs/py36/bin/python
 /home/leungi/miniconda3/envs/stooip/bin/python
 /home/leungi/miniconda3/envs/stooip-36/bin/python
 /home/leungi/miniconda3/bin/python
> pd = reticulate::import("pandas")
Error in py_module_import(module, convert = convert) :
  ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/leungi/miniconda3/envs/stooip-27/lib/python2.7/site-packages/pandas/_libs/window.so)

Detailed traceback:
  File "/home/leungi/miniconda3/envs/stooip-27/lib/python2.7/site-packages/pandas/__init__.py", line 42, in <module>
    from pandas.core.api import *
  File "/home/leungi/miniconda3/envs/stooip-27/lib/python2.7/site-packages/pandas/core/api.py", line 26, in <module>
    from pandas.core.groupby import Grouper
  File "/home/leungi/miniconda3/envs/stooip-27/lib/python2.7/site-packages/pandas/core/groupby/__init__.py", line 1, in <module>
    from pandas.core.groupby.groupby import GroupBy  # noqa: F401
  File "/home/leungi/miniconda3/envs/stooip-27/lib/python2.7/site-packages/pandas/core/groupby/groupby.py", line 37, in <module>
    from pandas.core.frame import DataFrame
  File "/home/leungi/miniconda3/envs/stooip-27/lib/python2.7/site-packages/pandas/core/frame.py", line 100, in <m
> q()
Save workspace image? [y/n/c]: n
[leungi@ohylpyt1-d /bin]$ bash
(base) bash-4.2$ conda activate stooip-27
(stooip-27) bash-4.2$ python
Python 2.7.16 |Anaconda, Inc.| (default, Sep 24 2019, 21:51:30)
[GCC 7.3.0] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas
>>>

System Info

[leungi@ohylpyt1-d /bin]$ uname -a
Linux ohylpyt1-d 3.10.0-514.6.1.el7.x86_64 #1 SMP Sat Dec 10 11:15:38 EST 2016 x86_64 x86_64 x86_64 GNU/Linux

Session Info

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.3 (Maipo)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.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_1.12

loaded via a namespace (and not attached):
[1] compiler_3.6.0  Matrix_1.2-17   Rcpp_1.0.1      grid_3.6.0
[5] jsonlite_1.6    lattice_0.20-38

[kevinushey]

  ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /home/leungi/miniconda3/envs/stooip-27/lib/python2.7/site-packages/pandas/_libs/window.so)

You likely need to configure your environment so that the version of the libstdc++ standard library bundled with Anaconda is loaded, rather than the default one on your system.

[leungi]

@kevinushey: thanks for prompt response and tip 😄

For future reference, followed this github issue and solved it.