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

Alex Chekholko chekh at stanford.edu
Mon Dec 17 17:31:04 PST 2012


Hi,

We have this page:

https://www.stanford.edu/group/farmshare/cgi-bin/wiki/index.php/R

Since we have a lot of R users and sometimes they want slightly 
different things and sometimes we switch OS releases on the corns, we 
have several R installs.  So check with R you use and what directories 
you load your libraries from.

E.g. we recently updated from Ubuntu 12.04 to 12.04.1 and that bumped R 
from 2.15 to 2.15.2, IIRC, but we have a differently compiled R in 
/mnt/glusterfs/software that was 2.15.x all along.

Please feel free to modify that wiki page if information is missing.


On 12/17/12 5:20 PM, Duncan Gillespie wrote:
> 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 <mailto:adalbert at stanford.edu>
>>
>> web: www.stanford.edu/~adalbert

-- 
Alex Chekholko chekh at stanford.edu 347-401-4860



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