R SIG Debian - Oct 2010 - [Rpy] "lapack routines cannot be loaded" in Ubuntu Linux 9.10

On 20 October 2010 at 09:57, Aman Thakral wrote:
| Thanks for your reply.  I just created a link to
| /usr/local/lib/R/lib/libRlapack.so in /usr/local/lib.  It works now.
| I'm just curious, is this the "right" way to do it? Is there a
better way?

I am coming to this a little late but ... it is a band aid to a self-inflicted
wound.

You only have libRlapack because you built R locally, with different settings
than the precompiled version.  See 

	http://cran.r-project.org/bin/linux/ubuntu

to read about current (ie R 2.12.0) versions for all Ubuntu releases.  This
is based on builds from the package sources of my (always current) Debian
packages. They work great -- I use them myself at work.

I know that Vincent and Michael also provide builds of rpy; if you ask nicely
they also rebuild rpy2 whenever I update it in Debian (which is essentially
whenever Laurent releases).  

I'll CC the r-sig-debian list which both of them read.

Cheers, Dirk
 
| Thanks,
| Aman
| 
| On Tue, Oct 19, 2010 at 5:26 PM, Laurent Gautier <lgautier at gmail.com>
wrote:
| 
| >  On 19/10/10 23:09, Aman Thakral wrote:
| >
| > Hi,
| >
| > I'm having some issues with LAPACK.  Here is the result of python -m
| > "rpy2.tests"
| >
| > rpy2 version 2.1.7
| >
| >
..............................................................................................................................getbuffer
| > .getbuffer
| >
| >
/usr/local/lib/python2.6/dist-packages/numpy-1.5.0b2-py2.6-linux-i686.egg/numpy
| >
| >
| > May be off-topic, but Numpy 1.5.0-release is available
| > (latest is 1.5.1rc1).
| >
| >
| > /core/numeric.py:284: RuntimeWarning: Item size computed from the PEP
3118
| > buffer format string does not match the actual item size.
| >   return array(a, dtype, copy=False, order=order)
| > .getbuffer
| > .getbuffer
| > .................................................Error in function (x,
| > symmetric, only.values = FALSE, EISPACK = FALSE)  :
| >   lapack routines cannot be loaded
| > In addition: Warning message:
| > In function (x, symmetric, only.values = FALSE, EISPACK = FALSE)  :
| >   unable to load shared object
'/usr/local/lib/R/modules//lapack.so':
| >   libRlapack.so: cannot open shared object file: No such file or
directory
| > E..Error in La.svd(x, nu, nv) : lapack routines cannot be loaded
| >
| >
| > I suspect a mismatch between the R installation rpy2 was compiled against
| > and the R installation this is run with.
| >
| > libRlapack.so should be in '/usr/local/lib/R/lib/' (but it is
not).
| >
| > Are you linkingR against a system-wide LAPACK ?
| >
| >
| >
| >
E.............................................................................................
| > =====================================================================|
> ERROR: testEigen (rpy2.robjects.tests.testArray.MatrixTestCase)
| > ----------------------------------------------------------------------
| > Traceback (most recent call last):
| >   File
| >
"/usr/local/lib/python2.6/dist-packages/rpy2-2.1.7_20101019-py2.6-linux-i686.egg/rpy2/robjects/tests/testArray.py",
| > line 91, in testEigen
| >     res = m.eigen()
| >   File
| >
"/usr/local/lib/python2.6/dist-packages/rpy2-2.1.7_20101019-py2.6-linux-i686.egg/rpy2/robjects/vectors.py",
| > line 457, in eigen
| >     res = self._eigen(self)
| > RRuntimeError: Error in function (x, symmetric, only.values = FALSE,
| > EISPACK = FALSE)  :
| >   lapack routines cannot be loaded
| >
| >
| > =====================================================================|
> ERROR: testSVD (rpy2.robjects.tests.testArray.MatrixTestCase)
| > ----------------------------------------------------------------------
| > Traceback (most recent call last):
| >   File
| >
"/usr/local/lib/python2.6/dist-packages/rpy2-2.1.7_20101019-py2.6-linux-i686.egg/rpy2/robjects/tests/testArray.py",
| > line 85, in testSVD
| >     res = m.svd()
| >   File
| >
"/usr/local/lib/python2.6/dist-packages/rpy2-2.1.7_20101019-py2.6-linux-i686.egg/rpy2/robjects/vectors.py",
| > line 447, in svd
| >     res = self._svd(self, nu = nu, nv = nv, LINPACK = False)
| > RRuntimeError: Error in La.svd(x, nu, nv) : lapack routines cannot be
| > loaded
| >
| >
| > ----------------------------------------------------------------------
| > Ran 275 tests in 3.655s
| >
| > FAILED (errors=2)
| >
| > I've tried to add the /usr/local/lib/R/bin folder to the path.  This
| > however, did not fix the issue.  Any help with this matter would be
greatly
| > appreciated.
| >
| > Thanks,
| > Aman
| >
| >
| >
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| >
| >
| >
| 
| 
| -- 
| Aman Thakral
| B.Eng & Biosci, M.Eng Design
| 
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-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com