rpy-list — Help, support and design discussion on RPy

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
> 

[Rpy] Module loading segfault?

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

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

[Rpy] rpy2-3.4.5 is released and on pypi

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.4.5 is released and on pypi. If using rpy2 in web app (e.g., with
Flask or Django) and annoying bug was fixed.

Release notes:
https://rpy2.github.io/doc/v3.4.x/html/changes.html#release-3-4-5

Best,


Laurent

[Rpy] rpy2-3.4.3 is released and on pypi

[Laurent G. <lga...@gm...>]

Hi,

rpy2 3.4.3, a bugfix release in the 3.4.x series, is released and on pypi.
Changes are listed here:
https://rpy2.github.io/doc/v3.4.x/html/changes.html#release-3-4-3

Best,

Laurent

[Rpy] rpy2-3.4.2 is release and on pypi

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.4.2 is released. This is a bugfix release mostly addressing an issue
with multithreading.
The changelog is here:
https://rpy2.github.io/doc/v3.4.x/html/changes.html#release-3-4-2

Best,

Laurent

[Rpy] rpy2-3.4.0 is released and on Pypi.

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.4.0 is released and on Pypi. In addition to the source package
binary wheels for MacOS (Python versions 3.7 and 3.8) are also made
available.

If using R-4.0 or greater and updated is recommended, and may be even
necessary.

The full changelog is in here:
https://rpy2.github.io/doc/v3.4.x/html/changes.html#release-3-4-0


Best,


Laurent

[Rpy] rpy2-3.3.6 is released and in pypi

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.3.6 is released an on pypi. This is a minor bugfix release with the
following changes:

 - The unit tests for importing R packages with `lib_loc` were broken
(issue #720).
 - Trying to create a memoryview for an R array with complex values was
failing with an attribute error.
 - Fix the constructor of metaclass
:class:`rpy2.robjects.methods.RS4Auto_Type`.
 - Fix call to end the embedded R in :class:`rpy2.robjects.R.__cleanup__`
(issue #734).

Best,

Laurent

[Rpy] rpy2-3.3.5 is released and on pypi

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.3.5 is released and on pypi. This bugfix release fixes just one but
annoying bug with the callback meant to capture input for R (that is R
asking for an user to enter an answer on the keyboard).

Laurent

[Rpy] rpy2-3.3.4 is released and on pypi.

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.3.4, a bugfix release in the 3.3.x series, is released and on pypi.

Laurent

[Rpy] rpy2-3.3.2 is released and on pypi.

[Laurent G. <lga...@gm...>]

Hi,
rpy2-3.3.2 is released and on pypi. The changelog is here:
https://rpy2.github.io/doc/v3.3.x/html/changes.html#release-3-3-2
Best,
Laurent

[Rpy] rpy2 3.3.0 and 3.3.1 are released and on pypi.

[Laurent G. <lga...@gm...>]

rpy2-3.3.0 and 3.3.1 are released and on pypi. This brings compatibility
with pandas >= 1.0. The Changelog is here:
https://rpy2.github.io/doc/v3.3.x/html/changes.html#release-3-3-1

[Rpy] Segfault issue with rpy2 3.2.7 under apache

[Wells O. <wel...@gm...>]

Hey guys, hope you can help. Ubuntu 18 LTS, upgraded R to 3.6.3, and now
rpy2 3.2.7 is segfaulting when called through Apache, but runs fine from
the command line.

Apache string: Apache/2.4.29 (Ubuntu) OpenSSL/1.1.1 mod_wsgi/4.5.17
Python/3.6 configured

This error pops up in the Apache logs about 100 times on a page load:

extern "Python": function _rinterface_cffi_api._processevents() called, but
@ffi.def_extern() was not called in the current subinterpreter.  Returning
0.

then it bombs with a segfault:

extern "Python": function _rinterface_cffi_api._processevents() called, but
@ffi.def_exter[Mon Apr 06 14:42:31.138806 2020] [core:notice] [pid 1104]
AH00051: child pid 31618 exit signal Segmentation fault (11), possible
coredump in /etc/apache2

Any ideas what might be happening here? I'm baffled.

-- 
Wells Oliver
wel...@gm... <wel...@gm...>

[Rpy] rpy2-3.2.7 is released and on pypi.

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.2.7 is released and on pypi. This is solely fixing a compatibility
issue with Python 3.5.
The next release will normally be rpy2-3.3.0, and should happen quite soon.

Best,

Laurent

Re: [Rpy] Deleting old doc pages for rpy2-2.0.x from Sourceforge

[Laurent G. <lga...@gm...>]

Actually I am deleting all rpy2 from Sourceforge (all is outdated / related
to too old releases).

Le dim. 26 janv. 2020 à 16:40, Laurent Gautier <lga...@gm...> a
écrit :

> Hi,
>
> The old doc pages for rpy2-2.0.x are being deleted from Sourceforge.
> Search engines are still returning these pages in results and this is
> creating confusion among users.
>
> Best,
>
> Laurent
>

[Rpy] Deleting old doc pages for rpy2-2.0.x from Sourceforge

[Laurent G. <lga...@gm...>]

Hi,

The old doc pages for rpy2-2.0.x are being deleted from Sourceforge. Search
engines are still returning these pages in results and this is creating
confusion among users.

Best,

Laurent

[Rpy] rpy2 3.2.5 is released.

[Laurent G. <lga...@gm...>]

#rpy2 <https://twitter.com/hashtag/rpy2?src=hashtag_click> 3.2.5 is
released and on pypi. It fixes a breaking change upstream (latest R package
`rlang`) and should make it work again with Python 3.5.

https://rpy2.github.io/doc/v3.2.x/html/changes.html#release-3-2-5
<https://t.co/PEOclwQobF?amp=1>

Re: [Rpy] rpy2-3.2.x is released and on Pypi.

[Laurent G. <lga...@gm...>]

rpy2-3.2.4 is out and on pypi, fixing a typo that prevented the ABI mode
from working.

Le sam. 14 déc. 2019 à 18:24, Laurent Gautier <lga...@gm...> a écrit :

> This is a bugfix release in the 3.2.x release. The only fix it contains is
> about a segfault sometimes occuring when parsing a R string that contains
> an error.
>

[Rpy] rpy2-3.2.x is released and on Pypi.

[Laurent G. <lga...@gm...>]

This is a bugfix release in the 3.2.x release. The only fix it contains is
about a segfault sometimes occuring when parsing a R string that contains
an error.

Re: [Rpy] rpy2-3.2.2 released and on pypi

[Laurent G. <lga...@gm...>]

[slightly less garbled version]

Hi,

rpy2-3.2.2 is released an on pypi. The only additional fixes compared to
3.2.1 are about better handling failure to build or install (now it tells
why it fails).

L.

Le dim. 3 nov. 2019 à 11:11, Laurent Gautier <lga...@gm...> a écrit :

> Hi,
>
> rpy2-3.2.2 is released an on pypi. The only additional fixes compared to
> 3.2.1 are better handle of failures of failure to build or install (now it
> tells why it fails).
>
> L.
>

[Rpy] rpy2-3.2.2 released and on pypi

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.2.2 is released an on pypi. The only additional fixes compared to
3.2.1 are better handle of failures of failure to build or install (now it
tells why it fails).

L.

[Rpy] rpy2-3.2.1 is released and on pypi.

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.2.1 is released and on pypi.This is the first bugfix release in the
3.2.x series, and the list of changes is here:
https://rpy2.github.io/doc/v3.2.x/html/changes.html#release-3-2-1

Best,

Laurent

[Rpy] rpy2-3.2.0 is released and on pypi

[Laurent G. <lga...@gm...>]

Hi,

rpy2-3.2.0 is released and on pypi. This fixes UTF-8 strings in R code, and
adds an optional #cffi API-mode interface to R. The list of changes is
here: https://rpy2.github.io/doc/v3.2.x/html/changes.html#release-3-2-0

Best,

Laurent

[Rpy] robjects

[Larry M. <lar...@gm...>]

I have code using version 2.8.6 that uses robjects, But in version 2.9
and higher that method does not seem to exist. Has the interface
changed?

[Rpy] rpy2-3.1.0 is released and on pypi

[Laurent G. <lga...@gm...>]

Hi,

Rpy2-3.1.0 is released and on pypi. If using the latest ggplot2 release,
multithreading, or pandas with NA values for integers or dates that's an
update you'll want to make now. A more complete changelog is in the doc as
usual: https://rpy2.github.io/doc/v3.1.x/html/changes.html#relase-3-1-0

L.

Re: [Rpy] Find a new home for the main source repository

[Luca B. <luc...@ma...>]

In data venerdì 23 agosto 2019 12:51:06 CEST, Laurent Gautier ha scritto:

Hello,
 
> Atlassian has announced the end of support for Mercurial repositories, so
> rpy2 will have to find a new home for its main source repository:

You might want to look at sourcehut.org.


-- 
Luca Beltrame, Ph.D.
Translational Genomics Unit, Department of Oncology
IRCCS Istituto di Ricerche Farmacologiche "Mario Negri"

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