[Rpy] undefined symbol: KillAllDevices

2008-05-12 Thread John Reid 
I get this error when I import rpy:
/usr/local/lib/python2.5/site-packages/_rpy2070.so: undefined symbol: 
KillAllDevices

   RPy module can not be imported. Please check if your rpy
   installation supports R 2.7.0. If you have multiple R versions
   installed, you may need to set RHOME before importing rpy. For
   example:

   >>> from rpy_options import set_options
   >>> set_options(RHOME='c:/progra~1/r/rw2011/')
   >>> from rpy import *




Compilation of rpy 1.0.2 and R 2.7.0 seems fine. I am on Suse Linux 10.3 
with gcc 4.1.2

Any ideas what I might be doing wrong?

Thanks,
John.


-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list

Re: [Rpy] undefined symbol: KillAllDevices

2008-05-12 Thread John Reid 
Well I seemed to have fixed it by changing the call to KillAllDevices() 
in rpymodule.c to Rf_KillAllDevices() as is defined in libR.so.

Perhaps there's a better way?

Thanks for a great rpy package BTW,
John.



John Reid wrote:
> I get this error when I import rpy:
> /usr/local/lib/python2.5/site-packages/_rpy2070.so: undefined symbol: 
> KillAllDevices
> 
>RPy module can not be imported. Please check if your rpy
>installation supports R 2.7.0. If you have multiple R versions
>installed, you may need to set RHOME before importing rpy. For
>example:
> 
>>>> from rpy_options import set_options
>>>> set_options(RHOME='c:/progra~1/r/rw2011/')
>>>> from rpy import *
> 
> 
> 
> 
> Compilation of rpy 1.0.2 and R 2.7.0 seems fine. I am on Suse Linux 10.3 
> with gcc 4.1.2
> 
> Any ideas what I might be doing wrong?
> 
> Thanks,
> John.
> 
> 
> -
> This SF.net email is sponsored by: Microsoft 
> Defy all challenges. Microsoft(R) Visual Studio 2008. 
> http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/


-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list

Re: [Rpy] undefined symbol: KillAllDevices

2008-05-12 Thread Gregory Warnes 

The fix for this bug has been submitted to SVN.

-G


On May 12, 2008, at 2:26PM , John Reid wrote:

Well I seemed to have fixed it by changing the call to  
KillAllDevices()

in rpymodule.c to Rf_KillAllDevices() as is defined in libR.so.

Perhaps there's a better way?

Thanks for a great rpy package BTW,
John.



John Reid wrote:
> I get this error when I import rpy:
> /usr/local/lib/python2.5/site-packages/_rpy2070.so: undefined  
symbol:

> KillAllDevices
>
>RPy module can not be imported. Please check if your rpy
>installation supports R 2.7.0. If you have multiple R  
versions
>installed, you may need to set RHOME before importing rpy.  
For

>example:
>
>>>> from rpy_options import set_options
>>>> set_options(RHOME='c:/progra~1/r/rw2011/')
>>>> from rpy import *
>
>
>
>
> Compilation of rpy 1.0.2 and R 2.7.0 seems fine. I am on Suse  
Linux 10.3

> with gcc 4.1.2
>
> Any ideas what I might be doing wrong?
>
> Thanks,
> John.
>
>
>  
-- 
---

> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/


-- 
---

This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list



-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list

[Rpy] [ rpy-Bugs-1961234 ] Hang on RPy exit when x11() graphics device is open

2008-05-12 Thread SourceForge.net 
Bugs item #1961234, was opened at 2008-05-09 17:22
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=453021&aid=1961234&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: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Gregory Warnes (warnes)
Assigned to: Nobody/Anonymous (nobody)
Summary: Hang on RPy exit when x11() graphics device is open

Initial Comment:
RPy hangs on exit when x11() graphics device is open with R 2.5.x and 2.6.x.

This simple code:

>>> from rpy import r
>>> r.plot(range(100))
>>> ^D

hangs R on Mac OSX 10.4.8.

Explicitly closing the graphics device before exiting python solves the problem.




--

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=453021&aid=1961234&group_id=48422

-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list

[Rpy] Another Mac install question

2008-05-12 Thread David Garfield 

Hey all,

  I'm trying to install RPy on my Mac (OS 4.11).  My version of R  
was installed from the pre-compiled binaries from CRAN (the one with  
the nice GUI attached), and hence I don't have access (or don't know  
how to access) R's source directory to carry out the (apparently)  
crucial:


(go to the R source directory)
make distclean
./configure --enable-R-shlib
make
make install


I found a previous thread on the mailing list (included below from  
July 31st of 2007), but I couldn't find an answer to the question.   
Is there anything I need to do to make sure that I have the shared  
libraries correct before installing RPy?


Cheers,

David


PREVIOUS MESSAGE
Hi

I have spent most of today trying to install rpy on my Mac  
(osx10.4.10). I
have python 2.5.1 and R version 2.5.0 (2007-04-23). Both work fine; R  
was
installed using the Precompiled binary distribution, python was  
installed

using the Pre-built packages installer from http://www.pythonmac.org/.

Has anybody ever managed to install rpy under these circumstances?

Any help gratefully received.

Many thanks

Mark-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list

Re: [Rpy] Another Mac install question

2008-05-12 Thread Gregory Warnes 


The standard Mac version of R includes the necessary shared library,  
hence it is not necesary to do this.  You should be able to simply run


cd /path/to/rpy/source/code/

python setup.py build

sudo python setup.py install

and everything should install properly, at least it does on my Mac  
OSX 10.4.11 box...


-G


On May 12, 2008, at 9:51PM , David Garfield wrote:


Hey all,

  I'm trying to install RPy on my Mac (OS 4.11).  My version of R  
was installed from the pre-compiled binaries from CRAN (the one  
with the nice GUI attached), and hence I don't have access (or  
don't know how to access) R's source directory to carry out the  
(apparently) crucial:


(go to the R source directory)
make distclean
./configure --enable-R-shlib
make
make install


I found a previous thread on the mailing list (included below from  
July 31st of 2007), but I couldn't find an answer to the question.   
Is there anything I need to do to make sure that I have the shared  
libraries correct before installing RPy?


Cheers,

David


PREVIOUS MESSAGE
Hi

I have spent most of today trying to install rpy on my Mac  
(osx10.4.10). I
have python 2.5.1 and R version 2.5.0 (2007-04-23). Both work fine;  
R was
installed using the Precompiled binary distribution, python was  
installed

using the Pre-built packages installer from http://www.pythonmac.org/.

Has anybody ever managed to install rpy under these circumstances?

Any help gratefully received.

Many thanks

Mark
-- 
---

This SF.net email is sponsored by: Microsoft
Defy all challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/ 



-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list

[Rpy] SF.net SVN: rpy: [513] trunk/rpy/setup.py

2008-05-12 Thread warnes 
Revision: 513
  http://rpy.svn.sourceforge.net/rpy/?rev=513&view=rev
Author:   warnes
Date: 2008-05-12 20:32:37 -0700 (Mon, 12 May 2008)

Log Message:
---
Add notes on what is necessary to build against multiple versions of R on OSX

Modified Paths:
--
trunk/rpy/setup.py

Modified: trunk/rpy/setup.py
===
--- trunk/rpy/setup.py  2008-05-10 13:30:40 UTC (rev 512)
+++ trunk/rpy/setup.py  2008-05-13 03:32:37 UTC (rev 513)
@@ -32,7 +32,7 @@
 
 DEBUG=True
 
-import os, os.path, sys, shutil
+import os, os.path, sys, shutil, re
 from distutils.core import setup, Extension
 from distutils.sysconfig import *
 from distutils.errors import *
@@ -66,6 +66,15 @@
 #if sys.platform=="win32":
 #rpy_wintools.CreatePythonWinLib()
 
+# On Mac OS X ("darwin") it is necessary to change the symlink
+#   /Library/Frameworks/R.framework/Versions/Current
+# to point to the current version of R in
+#  /Library/Frameworks/R.framework/Versions/X.Y
+# for that version of R to execute.  So, we need to store the original
+# symlink here so we can restore it when we are done
+if sys.platform=="darwin":
+  darwin_original_version = 
os.readlink("/Library/Frameworks/R.framework/Versions/Current")
+
 modules = []
 for RHOME in RHOMES:

@@ -87,6 +96,16 @@
 UNDEF = []
 
 # configure the R paths
+#if sys.platform=="darwin":
+#  version = 
+#  if os.symlink("/Library/Frameworks/R.framework/Versions/Current")
+#  if RHOME.endswith('/'):
+#RHOME = RHOME[:-1]
+#  print "RHOME=",os.path.join(os.path.dirname(RHOME),
+#  os.readlink(RHOME) )
+#  sys.exit()
+  
+
 RVERSION = rpy_tools.get_R_VERSION(RHOME, force_exec=True)
 RVER = rpy_tools.get_R_VERSION_CODE(RVERSION)
 


This was sent by the SourceForge.net collaborative development platform, the 
world's largest Open Source development site.

-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list

[Rpy] SF.net SVN: rpy: [514] trunk/rpy

2008-05-12 Thread warnes 
Revision: 514
  http://rpy.svn.sourceforge.net/rpy/?rev=514&view=rev
Author:   warnes
Date: 2008-05-12 20:47:51 -0700 (Mon, 12 May 2008)

Log Message:
---
Updated for 1.0.3

Modified Paths:
--
trunk/rpy/NEWS
trunk/rpy/rpy_version.py

Modified: trunk/rpy/NEWS
===
--- trunk/rpy/NEWS  2008-05-13 03:32:37 UTC (rev 513)
+++ trunk/rpy/NEWS  2008-05-13 03:47:51 UTC (rev 514)
@@ -1,3 +1,13 @@
+CHANGES IN RPY 1.0.3 - 2008-05-12
+-
+
+Bug fixes:
+
+- Correct issue with R 2.7.0. (R 2.7.0 exports the symbol 'Rf_KillAllDevices' 
+  instead of 'KillAllDevices')
+
+
+
 CHANGES IN RPY 1.0.2 - 2008-04-02
 -
 

Modified: trunk/rpy/rpy_version.py
===
--- trunk/rpy/rpy_version.py2008-05-13 03:32:37 UTC (rev 513)
+++ trunk/rpy/rpy_version.py2008-05-13 03:47:51 UTC (rev 514)
@@ -1 +1 @@
-rpy_version = "1.0.2"
+rpy_version = "1.0.3"


This was sent by the SourceForge.net collaborative development platform, the 
world's largest Open Source development site.

-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list

[Rpy] Version 1.0.3 now available

2008-05-12 Thread Gregory. R. Warnes 

Hi All,

I've just placed RPy 1.0.3 on SourceForge.  The primary purpose of  
this release is to provide support for R 2.7.0.


Sadly, the virtual machine I use for building Windows binary packages  
has become corrupted, so that I am unable to build the windows  
binary.  Can someone else build this for our Windows users?


Thanks

-Greg


Gregory R. Warnes, Ph.D.
Associate Professor
Center for Biodefence Immune Modeling
   and
Department of Biostatistics and Computational Biology
University of Rochester


-
This SF.net email is sponsored by: Microsoft 
Defy all challenges. Microsoft(R) Visual Studio 2008. 
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list