[Rpy] [ rpy-Bugs-2062627 ] R cannot initialize more than once in process
Bugs item #2062627, was opened at 2008-08-20 18:01
Message generated for change (Comment added) made by lgautier
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Category: Source
Group: rpy
Status: Open
>Resolution: Postponed
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Nobody/Anonymous (nobody)
Summary: R cannot initialize more than once in process
Initial Comment:
Hello,
I am currently working with a software package (ArcGIS) that runs Python “In
Process”. There has been a call from our users to be able to integrate R
functionality. Our “Out of Proc” version allows us to call rpy over and over
again because it is essentially re-initializing the R() instance on each run.
But when we switch it over to the “In Proc” version we get the following error
message:
Traceback (most recent call last):
File "", line 29, in
File "", line 8, in testPoly2Line
File "C:\Python25\lib\site-packages\rpy.py", line 346, in r = R()
File "C:\Python25\lib\site-packages\rpy.py", line 286, in __init__
_rpy.r_init(HAS_NUMERIC);
RuntimeError: Only one R object may be instantiated per session
The problem can be explained by the following set of issues: 1) We embed Python
in our application for use as a scripting engine, 2) Each time a Python script
is run in the application, it is from a new Python session (i.e. a brand new
set of locals and globals) but in the same process, 3) When importing the
Python R libraries, it binds the RPy .DLL into process, 4) In Python R�s
startup, there is a static integer in _rpy.r_init used as a flag that
determines if R has already been loaded. The rest of the function initializes
numeric if sent the flag to do so, and throws a RuntimeError if R was
initialized before. Since the library is still resident in memory even after
the Python session goes away, this stays set to 1. Looking at the C
implementation of the r_init function, this seems unnecessary and there have
been no ill effects from patching the Python to ignore the error. After a
cursory read over the Python, this appears to be a piece of legacy that isn�t
necessary anymore as it does not affect anything else.
We have a hack that allows us to run it In Proc and we wanted to know if it is
appropriate: (On Line ~ 286 of rpy.py)
try:
_rpy.r_init(HAS_NUMERIC)
except RuntimeError, e:
pass
_rpy.set_mode(NO_DEFAULT)
So in our case, RPython�s refusal to instantiate another instance of the R()
object by throwing a RuntimeError is considered a bug, because the binary
library is already initialized and resident in memory, its related Python
locals just went away and need to be allowed to reset. Ignoring the error is
idea, but warning instead of throwing is, at the very least, preferable.
Ideally the code in C would more resemble this:
static PyObject *
r_init(PyObject *self, PyObject *args)
{
static int first=1;
int i;
if (!PyArg_ParseTuple(args, "i:r_init", &i))
return NULL;
use_numeric = i;
if(first==1)
{
#ifdef WITH_NUMERIC
if(use_numeric)
init_numeric();
#endif
first=0;
}
Py_INCREF(Py_None);
return Py_None;
}
Thanks so much ahead of time. Best wishes,
MJ
Mark Janikas
Product Engineer
ESRI, Geoprocessing
380 New York St.
Redlands, CA 92373
909-793-2853 (2563)
[EMAIL PROTECTED]
--
>Comment By: lgautier (lgautier)
Date: 2008-09-19 08:35
Message:
Could provide version numbers for the version you tried ?
It was fixed for rpy2 few weeks ago.
>>> import rpy2.rinterface as ri
>>> ri.initr()
0
>>> ri.initr()
0
>>>
--
Comment By: Mark Janikas (mark_janikas)
Date: 2008-09-16 00:08
Message:
Just found the same error in RPy2.
: R can only be initialized once.
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[Rpy] [ rpy-Bugs-1956434 ] rpy 1.0~rc1segfault with bioconductor packages
Bugs item #1956434, was opened at 2008-05-02 22:42
Message generated for change (Comment added) made by lgautier
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Category: None
Group: None
Status: Open
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Faheem Mitha (fmitha)
Assigned to: Nobody/Anonymous (nobody)
Summary: rpy 1.0~rc1segfault with bioconductor packages
Initial Comment:
Hi,
I'm getting a segfault with rpy, 1.0~rc1-2 on Debian etch, with the CRAN
backport of 2.6.2.
Faheem.
**
Debian package info.
**
||/ NameVersion Description
+++-===-===-==
ii python-rpy 1.0~rc1-2 Python
interface to the GNU R language and environment
ii r-base-core 2.6.2-1~etchcran.1 GNU R core
of statistical computing language and environment
Script to reproduce
from rpy import r
r.library("affy")
r.library("hu6800cdf")
fnames = [u'AD8.CEL', u'L01.CEL', u'L02.CEL', u'L04.CEL', u'L05.CEL',
u'L06.CEL']
celdat = r.ReadAffy(filenames = fnames, celfile_path = 'data')
*
Run output
[EMAIL PROTECTED]:/tmp$ python rpy_bug.py
RHOME= /usr/lib64/R
RVERSION= 2.6.2
RVER= 2062
RUSER= /home/faheem
Loading Rpy version 2062 .. Done.
Creating the R object 'r' .. Done
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affyio
Loading required package: preprocessCore
Error: segfault from C stack overflow
Segmentation fault
R package info obtained from sessionInfo.
> sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L
C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] hu6800cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0
[4] affyio_1.6.1 Biobase_1.16.3
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
--
>Comment By: lgautier (lgautier)
Date: 2008-09-19 08:48
Message:
Seems to be working with rpy2 and R-2.7:
import rpy2.robjects as ro
ro.r.library("affy")
cel = ro.r["read.affybatch"]("GSM177882.CEL.gz")
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[Rpy] [ rpy-Bugs-1956434 ] rpy 1.0~rc1segfault with bioconductor packages
Bugs item #1956434, was opened at 2008-05-02 22:42
Message generated for change (Settings changed) made by lgautier
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=453021&aid=1956434&group_id=48422
Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
>Status: Closed
Resolution: Fixed
Priority: 5
Private: No
Submitted By: Faheem Mitha (fmitha)
Assigned to: Nobody/Anonymous (nobody)
Summary: rpy 1.0~rc1segfault with bioconductor packages
Initial Comment:
Hi,
I'm getting a segfault with rpy, 1.0~rc1-2 on Debian etch, with the CRAN
backport of 2.6.2.
Faheem.
**
Debian package info.
**
||/ NameVersion Description
+++-===-===-==
ii python-rpy 1.0~rc1-2 Python
interface to the GNU R language and environment
ii r-base-core 2.6.2-1~etchcran.1 GNU R core
of statistical computing language and environment
Script to reproduce
from rpy import r
r.library("affy")
r.library("hu6800cdf")
fnames = [u'AD8.CEL', u'L01.CEL', u'L02.CEL', u'L04.CEL', u'L05.CEL',
u'L06.CEL']
celdat = r.ReadAffy(filenames = fnames, celfile_path = 'data')
*
Run output
[EMAIL PROTECTED]:/tmp$ python rpy_bug.py
RHOME= /usr/lib64/R
RVERSION= 2.6.2
RVER= 2062
RUSER= /home/faheem
Loading Rpy version 2062 .. Done.
Creating the R object 'r' .. Done
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affyio
Loading required package: preprocessCore
Error: segfault from C stack overflow
Segmentation fault
R package info obtained from sessionInfo.
> sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L
C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] hu6800cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0
[4] affyio_1.6.1 Biobase_1.16.3
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
--
Comment By: lgautier (lgautier)
Date: 2008-09-19 08:48
Message:
Seems to be working with rpy2 and R-2.7:
import rpy2.robjects as ro
ro.r.library("affy")
cel = ro.r["read.affybatch"]("GSM177882.CEL.gz")
--
You can respond by visiting:
https://sourceforge.net/tracker/?func=detail&atid=453021&aid=1956434&group_id=48422
-
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
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