Re: [Rpy] Module loading segfault?

[Israel B. <ijb...@al...>]

More information for the below issue: I have now tried this on a variety of OS and Python configurations, with the only one that worked being Python3.8 on Ubuntu. In all cases, the install of R and the eseis module was new, with the install of eseis accomplished via running the “install.packages(‘eseis’)” command in R. Also, in all cases eseis loaded fine in R - it is only rpy2 that had issues with the library.

Configurations tried:

CentOS 7, python 3.6
Ubuntu 20, python 3.8
MacOS X Catalina 10.15.7 Python 3.9.5
MacOS X Catalina 10.15.7 Python 3.8.9
MacOS X Big Sur 11.2 Python 3.9.5
MacOS X Big Sur 11.2 Python 3.8.10

So from the test with ubuntu, I know this library *can* work, but most of the time it does not (unless I can figure out what’s different about the ubuntu install…Something about third-party shared libs, perhaps?)
---
Israel Brewster
Software Engineer
Alaska Volcano Observatory 
Geophysical Institute - UAF 
2156 Koyukuk Drive 
Fairbanks AK 99775-7320
Work: 907-474-5172
cell:  907-328-9145

> On Jun 17, 2021, at 1:11 PM, Israel Brewster <ijb...@al...> wrote:
> 
> A coworker of mine provided me with some R code that I need to integrate into my python code, for which purpose rpy2 appears to be ideal. Overall it seems to work as desired, except for when the code tries to use the “eseis” module. When trying to load (if that’s the correct terminology for R…) that one module, I get a segfault.
> 
> Loading the same module from an R session works fine, the segfault only occurs when loading through rpy2. Does anyone have any idea how I can fix this?
> 
> Python: 3.9.5 on Mac OS X Catalina 10.15.7
> R version 4.1.0
> rpy2 version 3.4.5
> 
> When loading library from python/rpy2:
> 
> Python 3.9.5 (v3.9.5:0a7dcbdb13, May  3 2021, 13:17:02) 
> [Clang 6.0 (clang-600.0.57)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from rpy2.robjects.packages import importr
> >>> importr('eseis')
> zsh: segmentation fault  python3.9
> 
> 
> But from R from the same console session:
> 
> 
> R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
> Copyright (C) 2021 The R Foundation for Statistical Computing
> Platform: x86_64-apple-darwin17.0 (64-bit)
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>   Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
> > library("eseis")
> Welcome to another bright 'eseis' session.
> > q()
> 
> ---
> Israel Brewster
> Software Engineer
> Alaska Volcano Observatory 
> Geophysical Institute - UAF 
> 2156 Koyukuk Drive 
> Fairbanks AK 99775-7320
> Work: 907-474-5172
> cell:  907-328-9145
>