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

Jason Bishop bishopj at stanford.edu
Mon Dec 17 18:42:12 PST 2012


In general, I would suggest using the locally maintained R if you are a heavy R user.

In this case, locally maintained R works for test case.  thank you Adrian.

jason



bishopj at corn20:~$ module load R-2.15.1-precise
bishopj at corn20:~$ cat lapack.r 
data(iris)
zz = lm(Sepal.Length ~., data = iris) 
summary(zz)

bishopj at corn20:~$ R --no-save < lapack.r 

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> data(iris)
> zz = lm(Sepal.Length ~., data = iris) 
> summary(zz)

Call:
lm(formula = Sepal.Length ~ ., data = iris)

Residuals:
     Min       1Q   Median       3Q      Max 
-0.79424 -0.21874  0.00899  0.20255  0.73103 

Coefficients:
                  Estimate Std. Error t value Pr(>|t|)    
(Intercept)        2.17127    0.27979   7.760 1.43e-12 ***
Sepal.Width        0.49589    0.08607   5.761 4.87e-08 ***
Petal.Length       0.82924    0.06853  12.101  < 2e-16 ***
Petal.Width       -0.31516    0.15120  -2.084  0.03889 *  
Speciesversicolor -0.72356    0.24017  -3.013  0.00306 ** 
Speciesvirginica  -1.02350    0.33373  -3.067  0.00258 ** 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Residual standard error: 0.3068 on 144 degrees of freedom
Multiple R-squared: 0.8673,	Adjusted R-squared: 0.8627 
F-statistic: 188.3 on 5 and 144 DF,  p-value: < 2.2e-16 

> 
> 


----- Original Message -----
From: "Adrian Albert" <adalbert at stanford.edu>
To: "bishopj" <bishopj at stanford.edu>, "Open discussion for users of FarmShare" <farmshare-discuss at lists.stanford.edu>
Sent: Monday, December 17, 2012 6:21:48 PM
Subject: Re: [farmshare-discuss] error in R installation on farmshare (corn)?

Thanks all for the replies! 


Here are the R commands that induce the error on my corn account: 


data(iris) 
zz = lm(Sepal.Length ~., data = iris) 
summary(zz) 


Note that this happens when using the default R available on the corn machines. To make that go away I found two solutions: 


1 ) I installed R from the sources in my home directory, ran that local copy, and the error disappeared. A bit of a hack though. 


2) I typed 
module load R.2.15.1-precise 
and then started R, as describe in https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/R 


Cheers, 
Adrian 


On Mon, Dec 17, 2012 at 5:31 PM, bishopj < bishopj at stanford.edu > wrote: 



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