Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Duncan Gillespie d.gillespie at stanford.edu
Mon Dec 17 17:20:00 PST 2012


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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/farmshare-discuss/attachments/20121217/6239c9d3/attachment.html>


More information about the farmshare-discuss mailing list