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

Adrian Albert adalbert at stanford.edu
Mon Dec 17 18:21:48 PST 2012


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
>
>
>  _______________________________________________
> farmshare-discuss mailing list
> farmshare-discuss at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
>
>
>
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> farmshare-discuss mailing list
> farmshare-discuss at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/farmshare-discuss
>



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