[Rpy] Python crashing
Whenever I plot in python, R crashes after a few seconds. I see the graph, everything seems to work fine, but then it just crashes. It is my understanding that gcc now prevents buffer overflows and generates this error. My error is below: Error during wrapup: C stack usage is too close to the limit *** stack smashing detected ***: python terminated Aborted Thanks, j P.S. in Ubuntu Feisty Fawn, after I install python-rpy, I only have the _rpy2040.so file, when I should have the _rpy2041.so file since I have R version 2.4.1. To overcome this, I changed rpy.py so that RVER=2040, so that it will actually work. - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] Python crashing
Okay, that's fine. I ignored the consistency check because it is a sub-point release, probably changing just a couple unimportant things in R. I'm now using the correct version, but I still get the same error when I, say, resize the window of a plot. Any reason? Thanks, j On 2/19/07, Gregory. R. Warnes <[EMAIL PROTECTED]> wrote: Hi Joseph, It really is essential that RPy is compiled against the exact version of R you are using. Modifying the source code to avoid the consistency check is likely to lead to segfaults like the ones you are seeing. Please upgrade to a newer version of Rpy to match your version of R. -G On Feb 17, 2007, at 3:25PM , Joseph Perla wrote: > Whenever I plot in python, R crashes after a few seconds. I see > the graph, everything seems to work fine, but then it just > crashes. It is my understanding that gcc now prevents buffer > overflows and generates this error. My error is below: > > Error during wrapup: C stack usage is too close to the limit > *** stack smashing detected ***: python terminated > Aborted > > Thanks, > j > > P.S. in Ubuntu Feisty Fawn, after I install python-rpy, I only > have the _rpy2040.so file, when I should have the _rpy2041.so file > since I have R version 2.4.1. To overcome this, I changed rpy.py > so that RVER=2040, so that it will actually work. > -- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] Python crashing
Yes, that seems to be the same problem I have. I confirm that the problem occurs whenever part of the graph window is not in view (including switching desktops). It also occurs when I resize the window even if it is not obscured. I am using Ubuntu Feisty Fawn with all the latest packages and an _rpy2041.so from some rpm online. I am using nVidia drivers. Is someone working on the problem, or do you just run scripts that output to .ps files? j On 2/19/07, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: On 19 February 2007 at 13:58, Joseph Perla wrote: | Okay, that's fine. I ignored the consistency check because it is a | sub-point release, probably changing just a couple unimportant things in R. | | I'm now using the correct version, but I still get the same error when I, | say, resize the window of a plot. Any reason? I think we may have the same issue logged as http://bugs.debian.org/401670 and to the best of my knowledge, no fix has been put forward. Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] tune object convertion
Hi everyone,
Just to let you know about a little bug. On a fresh install of Ubuntu
Feisty (7.04), I apt-get install python-rpy which installs all
dependencies. Whet I fire up Python and import rpy, I get this error:
RHOME= /usr/lib/R
RVERSION= 2.4.1
RVER= 2041
RUSER= /home/joe
Loading Rpy version 2041 ..
Traceback (most recent call last):
File "", line 1, in
File "/usr/lib/python2.5/site-packages/rpy.py", line 112, in
exec("import _rpy%s as _rpy" % RVER)
File "", line 1, in
ImportError: No module named _rpy2041
The rpy2041 module does not exist. My solution is to google an rpm with the
file inside, extract it, and place it in the approprate folder on my
installation. Everything works after that. I do not, however, think this
should be the default behaviour.
I believe this is may be the problem to which someone recently filed a bug
report, for which you wanted a more detailed description. I have not
confirmed this missing file for other systems.
Thanks,
j
-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share your
opinions on IT & business topics through brief surveys-and earn cash
http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] tune object convertion
No, that doesn't seem to be it. Both folders only have _rpy2040.so, when my version of R is clearly 2.4.1. My python2.5 site-packages actually has more files related to rpy than 2.4. In any case, this is a simple problem to remedy. Just include the _rpy2041.so with the package. I imagine it will help a lot of people out. j - Try using python2.4, not python2.5. Python 2.5 is not yet suppported by the automated build of Python modules from Python module sources. At least not on Debian. I am not entirely sure exactly what Ubuntu does to the RPy and R packages I maintain for Debina ... as they never communicate back. It *may* well be that they try to support Python 2.5 automatically; I just don't know if include RPy. On my Debian testing system, the directory /usr/lib/python2.5/site-packages is empty whereas /usr/lib/python2.4/site-packages contains the on-install autobuilt files, incl rpy's. What does Feisty have? Dirk | The rpy2041 module does not exist. My solution is to google an rpm with the | file inside, extract it, and place it in the approprate folder on my | installation. Everything works after that. I do not, however, think this | should be the default behaviour. | - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] tune object convertion
No, that doesn't seem to be it. Both folders only have _rpy2040.so, when my version of R is clearly 2.4.1. My python2.5 site-packages actually has more files related to rpy than 2.4. In any case, this is a simple problem to remedy. Just include the _rpy2041.so with the package. I imagine it will help a lot of people out. j Try using python2.4, not python2.5. Python 2.5 is not yet suppported by the automated build of Python modules from Python module sources. At least not on Debian. I am not entirely sure exactly what Ubuntu does to the RPy and R packages I maintain for Debina ... as they never communicate back. It *may* well be that they try to support Python 2.5 automatically; I just don't know if include RPy. On my Debian testing system, the directory /usr/lib/python2.5/site-packages is empty whereas /usr/lib/python2.4/site-packages contains the on-install autobuilt files, incl rpy's. What does Feisty have? Dirk | The rpy2041 module does not exist. My solution is to google an rpm with the | file inside, extract it, and place it in the approprate folder on my | installation. Everything works after that. I do not, however, think this | should be the default behaviour. | - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] tune object convertion
Okay, https://launchpad.net/ubuntu/+source/rpy/+bug/93924 . Thanks, j On 3/19/07, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: On Mon, Mar 19, 2007 at 02:17:05PM -0400, Joseph Perla wrote: > No, that doesn't seem to be it. Both folders only have _rpy2040.so, when my > version of R is clearly 2.4.1. My python2.5 site-packages actually has more > files related to rpy than 2.4. > > In any case, this is a simple problem to remedy. Just include the > _rpy2041.so with the package. I imagine it will help a lot of people out. Yes, that is what we do for Debian. If you file an Ubuntu bug report for rpy, an updated (and corrected) Ubuntu package may get produced, Dirk > j > - > Try using python2.4, not python2.5. Python 2.5 is not yet suppported by the > > automated build of Python modules from Python module sources. > > At least not on Debian. I am not entirely sure exactly what Ubuntu does to > the RPy and R packages I maintain for Debina ... as they never communicate > back. It *may* well be that they try to support Python 2.5automatically; I > just don't know if include RPy. On my Debian testing system, the directory > >/usr/lib/python2.5/site-packages > > is empty whereas > >/usr/lib/python2.4/site-packages > > contains the on-install autobuilt files, incl rpy's. What does Feisty have? > > Dirk > | The rpy2041 module does not exist. My solution is to google an rpm with > the > | file inside, extract it, and place it in the approprate folder on my > | installation. Everything works after that. I do not, however, think this > | should be the default behaviour. > | > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > ___ > rpy-list mailing list > rpy-list@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rpy-list -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
Re: [Rpy] tune object convertion
Okay, https://launchpad.net/ubuntu/+source/rpy/+bug/93924 . j On 3/19/07, Dirk Eddelbuettel <[EMAIL PROTECTED]> wrote: On Mon, Mar 19, 2007 at 02:17:05PM -0400, Joseph Perla wrote: > No, that doesn't seem to be it. Both folders only have _rpy2040.so, when my > version of R is clearly 2.4.1. My python2.5 site-packages actually has more > files related to rpy than 2.4. > > In any case, this is a simple problem to remedy. Just include the > _rpy2041.so with the package. I imagine it will help a lot of people out. Yes, that is what we do for Debian. If you file an Ubuntu bug report for rpy, an updated (and corrected) Ubuntu package may get produced, Dirk > j > - > Try using python2.4, not python2.5. Python 2.5 is not yet suppported by the > > automated build of Python modules from Python module sources. > > At least not on Debian. I am not entirely sure exactly what Ubuntu does to > the RPy and R packages I maintain for Debina ... as they never communicate > back. It *may* well be that they try to support Python 2.5automatically; I > just don't know if include RPy. On my Debian testing system, the directory > >/usr/lib/python2.5/site-packages > > is empty whereas > >/usr/lib/python2.4/site-packages > > contains the on-install autobuilt files, incl rpy's. What does Feisty have? > > Dirk > | The rpy2041 module does not exist. My solution is to google an rpm with > the > | file inside, extract it, and place it in the approprate folder on my > | installation. Everything works after that. I do not, however, think this > | should be the default behaviour. > | > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > ___ > rpy-list mailing list > rpy-list@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rpy-list -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV ___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV___ rpy-list mailing list rpy-list@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rpy-list
