rpy import error at Gusty

[sundol]

Binary package hint: python-rpy

"import rpy" of python gives an error

How to reproduce and error message are following
****************

myid@mypc:~$ python
Python 2.5.1 (r251:54863, Jul 17 2007, 15:55:37)
[GCC 4.1.3 20070629 (prerelease) (Ubuntu 4.1.2-13ubuntu2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
RHOME= /usr/lib/R
RVERSION= 2.5.1
RVER= 2051
RUSER= /home/hckim
Loading Rpy version 2051 ..
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/rpy.py", line 112, in <module>
    exec("import _rpy%s as _rpy" % RVER)
  File "<string>", line 1, in <module>
ImportError: No module named _rpy2051
>>>

TEST CASE:
1) Install python-rpy
2) Open a terminal and execute python interpreter
3) Launch "import rpy" from python interpreter
4) The above traceback raises

[sundol (hyunchul-love-me-deactivatedaccount-deactivatedaccount-deactivatedaccount)]

This bug happens whenever the version of R has been updated with same error message of "No module named _rpy20XX".
I hope that this problem, somehow, will be solved automatically when R has been updated.

Thanks.

[Luís Figueira (lafig3)]

This bug still exists in the gutsy release version. I've also tried to update R, but without any success. Anybody knows how to fix this?

Python 2.5.1 (r251:54863, Oct 5 2007, 13:36:32)
[GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
RHOME= /usr/lib/R
RVERSION= 2.5.1
RVER= 2051
RUSER= /home/luisf
Loading Rpy version 2051 ..
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/rpy.py", line 112, in <module>
    exec("import _rpy%s as _rpy" % RVER)
  File "<string>", line 1, in <module>
ImportError: No module named _rpy2051

[sundol (hyunchul-love-me-deactivatedaccount-deactivatedaccount-deactivatedaccount)]

Hi,

It will work with older version of R because gutsy and feisty have _rpy2041
or _rpy2050.
For sure, try "slocate _rpy".
I got
/usr/lib/python2.5/site-packages/_rpy2041.so
/usr/lib/python2.4/site-packages/_rpy2041.so
and you maybe get these, too.
If you get _rpy2041 or _rpy2050, R 2.4.1 or R 2.5.0 will work well,
respectively.

Best,
Hyunchul

On 10/21/07, la-figueira <email address hidden> wrote:
>
> This bug still exists in the gutsy release version. I've also tried to
> update R, but without any success. Anybody knows how to fix this?
>
> Python 2.5.1 (r251:54863, Oct 5 2007, 13:36:32)
> [GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
> >>> import rpy
> RHOME= /usr/lib/R
> RVERSION= 2.5.1
> RVER= 2051
> RUSER= /home/luisf
> Loading Rpy version 2051 ..
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/usr/lib/python2.5/site-packages/rpy.py", line 112, in <module>
> exec("import _rpy%s as _rpy" % RVER)
> File "<string>", line 1, in <module>
> ImportError: No module named _rpy2051
>
> --
> rpy import error at Gusty
> https://bugs.launchpad.net/bugs/128180
> You received this bug notification because you are a direct subscriber
> of the bug.
>

[Joel Nelson (joelnn)]

Just adding my vote to get this fixed, I ran into it today

[Diwaker Gupta (diwaker)]

I can confirm this bug. I tried building from source but that doesn't help much. Does anyone know a fix?

[Diwaker Gupta (diwaker)]

I found a (temporary) solution:

- Download the sources from rpy.sf.net
- Make sure you have all dependencies installed (sudo apt-get install r-base-dev python-all-dev)
- Modify setup.py, line 132 as follows:
include_dirs = [ os.path.join(RHOME.strip(), 'include'), '/usr/share/R/include/',
- export RHOMES=/usr/lib/R
- run 'python setup.py build'
- copy build/lib.linux-i686-2.5/_rpy2051.so to /usr/lib/python-2.5/site-packages

Thats it!

[sundol (hyunchul-love-me-deactivatedaccount-deactivatedaccount-deactivatedaccount)]

Thank you. It works!!

Just, here is a correction of single typo-error.
From:
/usr/lib/python-2.5/site-packages
To:
/usr/lib/python2.5/site-packages

On 11/1/07, Diwaker Gupta <email address hidden> wrote:
>
> I found a (temporary) solution:
>
> - Download the sources from rpy.sf.net
> - Make sure you have all dependencies installed (sudo apt-get install
> r-base-dev python-all-dev)
> - Modify setup.py, line 132 as follows:
> include_dirs = [ os.path.join(RHOME.strip(), 'include'),
> '/usr/share/R/include/',
> - export RHOMES=/usr/lib/R
> - run 'python setup.py build'
> - copy build/lib.linux-i686-2.5/_rpy2051.so to /usr/lib/python-2.5
> /site-packages
>
> Thats it!
>
> --
> rpy import error at Gusty
> https://bugs.launchpad.net/bugs/128180
> You received this bug notification because you are a direct subscriber
> of the bug.
>

[Martin Saturka (kvutza)]

Another temporary solution is getting the library from the Debian package:
http://packages.debian.org/testing/python/python-rpy

May be, the python-rpy dependences on r-base-core should be with '=='
and not with '>=' specifier.

[Guy Mauve (cesium5500)]

Same thing... HOPE it will be fix soon, it drive you seek when you spend you spend a whole day trying to make it work instead coding with...

Thanks for all the good Work anyway!

[Casey Greene (casey-s-greene)]

I just ran into this today too using amd64 gutsy. I'd love to see it fixed. The version from debian is a successful workaround for me.

[CTW (ctw)]

I have the same problem ... very annoying.

[Lorenzki (lorenz-gerber)]

Same problem here, on Gutsy.

[Brandon King (kingb)]

Same problem on Gutsy and it's Jan 9th, 2008... Anyone know why this hasn't been fixed as of yet?

[Ben Stone (benjamin-stone)]

me too (on gutsy)

[Green (green-peas)]

In addition to the solution posted by Diwaker Gupta, I found that the source code in rpy.py file needs to be changed:

Specifically, line 168 should be changed from

RException = _rpy.RException

to

RException = _rpy.RPy_RException.

Once this done, open a new python interpreter session and type

import rpy

You should that rpy is loaded without any errors

[Green (green-peas)]

I meant to type "You should find that rpy is loaded without any errors".

[nosolosw (nosolosw)]

Like https://bugs.launchpad.net/ubuntu/+source/rpy/+bug/128180/comments/3 (sundol) says ubuntu gutsy haven't _rpy2051. Because this i tried install R 2.5.0 and run it with python 2.5.1 and python-rpy packages... and it goes. Next ones are steps i followed:

 --- 1. Preparing environment:
cd ~/downloads
wget http://cran.es.r-project.org/src/base/R-2/R-2.5.0.tar.gz # download package
sudo apt-get install libxt-dev xorg-dev libX11-dev # install required libraries

 --- 2. Installing R 2.5.0 from sources:

tar -xvvzf R-2.5.0.tar.gz
cd R-2.5.0
./configure --enable-R-shlib
make
make check
make install

 --- 3. Linking RHOME and libraries properly:

export RHOME=/usr/local/bin/R

cd /usr/lib
sudo ln -s ../local/
sudo ln -s ../local/lib/R/lib/libR.so .
sudo ln -s ../local/lib/R/lib/libRblas.so .
sudo ln -s ../local/lib/R/lib/libRlapack.so .

Last step is required because i have two R versions (R 2.5.0 and R 2.5.1). If you don't link to R 2.5.0 version it try to link with R 2.5.1 ... and it doesn't run.

Finally, run python ... and rpy imports! :)

[Casey Greene (casey-s-greene)]

Can we get the importance of this bumped up? This is obviously annoying a lot of people and there seem to be a number of fixes available for implementation.

[Gabriel (notelab)]

I would be very grateful if this could be fixed.

[Greg Detre (greg-gregdetre)]

I'd love to be able to use RPy too, but I'm coming up against the same bug :(

[Greg Detre (greg-gregdetre)]

Thank you, Diwaker, Sundol and Green! One small note - for the latest version of the source that i downloaded from rpy.sf.net, the line number to change is now 145, not 132. It's easy enough to find - it looks like this:

    else: # unix-like systems, this is known to work for Linux and Solaris
        # include_dirs = [ os.path.join(RHOME.strip(), 'include'),
        # 'src', '/usr/share/R/include' ]
        # modified by gjd as per https://bugs.launchpad.net/ubuntu/+source/rpy/+bug/128180
        include_dirs = [ os.path.join(RHOME.strip(), 'include'), '/usr/share/R/include/',
                         'src', '/usr/share/R/include' ]
        libraries=['R','Rlapack']

[Iain Russell (irussell30)]

Does anyone know if this has been fixed in the new release "Hardy Heron", 8.04 ? I'm wondering whether to try one of the workarounds already documented, or simply install the beta version of Hardy and see if it works..

Thanks
Iain

[sundol (hyunchul-love-me-deactivatedaccount-deactivatedaccount-deactivatedaccount)]

It worked well in alpha version but not now in beta version.
I think that they couldn't fix this bug.

_rpy2061.so exists but R version is 2.62 and it produces same error messages.

Hyunchul

On Wed, Mar 26, 2008 at 10:53 PM, Iain Russell <email address hidden> wrote:
> Does anyone know if this has been fixed in the new release "Hardy
> Heron", 8.04 ? I'm wondering whether to try one of the workarounds
> already documented, or simply install the beta version of Hardy and see
> if it works..
>
> Thanks
> Iain
>
>
>
> --
> rpy import error at Gusty
> https://bugs.launchpad.net/bugs/128180
> You received this bug notification because you are a direct subscriber
> of the bug.
>

[Iain Russell (irussell30)]

Thanks; in the end I got it to work by building the _rpy2051.so library from source using the steps described by Diwakar Gupta on 31 Oct. 2007.

In the next month or so (when the production release comes out) I will install Hardy which means, I guess, that I'll have to do the same again since it looks like R is at version 2.6.2 but the rpy library for Ubuntu is still at 2.6.1

Thanks for the information...
Iain

[Allen Riddell (ariddell)]

I'll just confirm that it does indeed exist in hardy beta right now.

[Sagar Mittal (sagar-mittal)]

This bug is still in Gutsy as of April 11. I've attached a .deb for Python 2.5.1 and R 2.5.1 on amd64.

[Diwaker Gupta (diwaker)]

Still exists in Hardy Heron. I've filed a new bug report:
https://bugs.launchpad.net/ubuntu/+source/rpy/+bug/223777

[Javier Rovegno Campos (jrovegno)]

I can confirm this bug on Feisty.
 I've update r from http://cran.r-project.org/bin/linux/ubuntu/
and I get this:

MyUSER@MyHOST:~$ python
Python 2.5.1 (r251:54863, Mar 7 2008, 03:41:45)
[GCC 4.1.2 (Ubuntu 4.1.2-0ubuntu4)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
RHOME= /usr/lib/R
RVERSION= 2.7.0
RVER= 2070
RUSER= /home/MyUSER
Loading Rpy version 2070 ..
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/rpy.py", line 112, in <module>
    exec("import _rpy%s as _rpy" % RVER)
  File "<string>", line 1, in <module>
ImportError: No module named _rpy2070

[Javier Rovegno Campos (jrovegno)]

Today I've upgrade python-rpy , r-cran-boot and r-cran-vr from http://cran.r-project.org/bin/linux/ubuntu/
And the problem had solved in Feisty
upgrade python-rpy 1.0~rc1-5 1.0.2-1feisty0
upgrade r-cran-boot 1.2.32-1feisty0 1.2.33-1feisty0
upgrade r-cran-vr 7.2.41-1feisty0 7.2.42-1feisty0

Now I had this results:
$ ls /usr/lib/python2.5/site-packages/_rpy*
/usr/lib/python2.5/site-packages/_rpy2070.so

$ python -c "import rpy"
$

Thanks

[netzberg (netzberg)]

Similar problem (see below) on Hardy Heron can be resolved by installing the following packages:
http://cran.r-project.org/bin/linux/ubuntu/hardy/r-base-core_2.7.0-1hardy0_i386.deb
http://cran.r-project.org/bin/linux/ubuntu/hardy/python-rpy_1.0.3-1hardy0_i386.deb
(ignore warnings "An older version is available in a software channel")

This will create /usr/lib/python2.5/site-packages/_rpy2070.so which will be accepted by rpy import.

--------------------

The original behaviour:

$ python
Python 2.5.2 (r252:60911, Apr 21 2008, 11:12:42)
[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/rpy.py", line 134, in <module>
    """ % RVERSION)
RuntimeError: No module named _rpy2062

      RPy module can not be imported. Please check if your rpy
      installation supports R 2.6.2. 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 *

[Luca Falavigna (dktrkranz)]

Intrepid is already fixed, autosyncs were rebuilt on a up-to-date r-base.
Hardy is affected: a rebuild against r-base 2.6.2-2 will fix this.
Gutsy is affected: a rebuild against r-base 2.5.1-1 will fix this.
Feisty is not affected.
Dapper is not affected.

[Luca Falavigna (dktrkranz)]

Version 1.0.1-1ubuntu1.1 uploaded to hardy-proposed.
Version 1.0~rc1-6ubuntu0.1 uploaded to gutsy-proposed.

[JamesLavin (james-patriotsbook)]

I've been having this same problem (on Hardy + R 2.6.2), but this new update fixed my problem.

Wonderful.

--James

[Jonathan Riddell (jr)]

accepted 1.0~rc1-6ubuntu0.1 into gutsy-proposed and 1.0.1-1ubuntu1.1 into hardy-proposed, please test.

[Luca Falavigna (dktrkranz)]

HARDY VERIFICATION

Using version 1.0.1-1ubuntu1 from hardy-release:
Python 2.5.2 (r252:60911, May 7 2008, 15:19:09)
[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/rpy.py", line 134, in <module>
    """ % RVERSION)
RuntimeError: No module named _rpy2062
      RPy module can not be imported. Please check if your rpy
      installation supports R 2.6.2. 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 *
>>>

Using version 1.0.1-1ubuntu1.1 from hardy-proposed:
Python 2.5.2 (r252:60911, May 7 2008, 15:19:09)
[GCC 4.2.3 (Ubuntu 4.2.3-2ubuntu7)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
>>>

[Luca Falavigna (dktrkranz)]

GUTSY VERIFICATION

Using version 1.0~rc1-6 from gutsy-release:
Python 2.5.1 (r251:54863, Mar 7 2008, 04:10:12)
[GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
RHOME= /usr/lib/R
RVERSION= 2.5.1
RVER= 2051
RUSER= /root
Loading Rpy version 2051 ..
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.5/site-packages/rpy.py", line 112, in <module>
    exec("import _rpy%s as _rpy" % RVER)
  File "<string>", line 1, in <module>
ImportError: No module named _rpy2051
>>>

Using version 1.0~rc1-6ubuntu0.1 from gutsy-proposed:
Python 2.5.1 (r251:54863, Mar 7 2008, 04:10:12)
[GCC 4.1.3 20070929 (prerelease) (Ubuntu 4.1.2-16ubuntu2)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import rpy
RHOME= /usr/lib/R
RVERSION= 2.5.1
RVER= 2051
RUSER= /root
Loading Rpy version 2051 .. Done.
Creating the R object 'r' .. Done
>>>

[Martin Pitt (pitti)]

Copied to hardy-updates.