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[farmshare-discuss] error in R installation on farmshare (corn)?

bishopj bishopj at stanford.edu
Mon Dec 17 17:31:07 PST 2012


Can somebody post an r script which reproduces the error.

Thanks




-------- Original message --------
From: Duncan Gillespie <d.gillespie at stanford.edu> 
Date: 12/17/2012  5:20 PM  (GMT-08:00) 
To: Open discussion for users of FarmShare <farmshare-discuss at lists.stanford.edu> 
Subject: Re: [farmshare-discuss] error in R installation on farmshare (corn)? 
 
This looks like a problem I had too and, although I don't know for sure, concluded it was due to an error in the path that R uses to find a required library or part of a library. I solved it by installing a local version of R in my home directory and using that instead of the central installation. That seemed to overcome the inconsistency producing the error.
Duncan


On 17 Dec 2012, at 17:09, Adrian Albert wrote:

Hello,

perhaps some of the R wizards on this list can help me with the following error. I connect to corn via ssh -X, I start R in command line, then try to do a very simple linear regression using lm(). However it seems that the R installation on farmshare is broken? It seems not to find lapack.so, which lm needs to perform a Cholesky inversion! Anyone knows why that is the case ? I attach a code snippet below.

Thanks!
Adrian

> data(iris)
> head(iris) 
  Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1          5.1         3.5          1.4         0.2  setosa
2          4.9         3.0          1.4         0.2  setosa
3          4.7         3.2          1.3         0.2  setosa
4          4.6         3.1          1.5         0.2  setosa
5          5.0         3.6          1.4         0.2  setosa
6          5.4         3.9          1.7         0.4  setosa
> 
> zz = lm(Sepal.Length ~., data = iris)
> summary(zz)
Error in chol2inv(Qr$qr[p1, p1, drop = FALSE]) : 
  lapack routines cannot be loaded
In addition: Warning message:
In chol2inv(Qr$qr[p1, p1, drop = FALSE]) :
  unable to load shared object '/usr/lib/R/modules//lapack.so':
  /usr/lib/R/modules//lapack.so: undefined symbol: dpstrf_
> 


-- 
---------------------------------------------------------------------
Adrian Albert
PhD Candidate, Electrical Engineering
Stanford University
Tel.: 001 510 213 1220
email: adalbert at stanford.edu

web:   www.stanford.edu/~adalbert


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