[R] Installing quantreg package under Ubuntu

[William Dunlap]

> -----Original Message-----
> From: Frank E Harrell Jr [mailto:f.harrell at vanderbilt.edu] 
> Sent: Tuesday, August 18, 2009 5:20 AM
> To: Ben Bolker
> Cc: r-help at r-project.org; William Dunlap; roger koenker
> Subject: Re: [R] Installing quantreg package under Ubuntu
> 
> Ben Bolker wrote:
> > 
> > 
> > Frank E Harrell Jr wrote:
> >> Does any have installation instructions for this?  When I run 
> >> install.packages('quantreg') I get:
> >>
> >> gcc -std=gnu99 -shared -o quantreg.so akj.o boot.o brute.o 
> chlfct.o 
> >> cholesky.o combos.o crq.o crqfnb.o dsel05.o etime.o 
> extract.o idmin.o 
> >> iswap.o kuantile.o mcmb.o penalty.o powell.o rls.o rq0.o 
> rq1.o rqbr.o 
> >> rqfn.o rqfnb.o rqfnc.o sparskit2.o srqfn.o srqfnc.o 
> srtpai.o -llapack 
> >> -lblas -lgfortran -lm -lgfortran -lm -L/usr/lib/R/lib -lR
> >> /usr/bin/ld: cannot find -llapack
> >>
> >>
> >>  > sessionInfo()
> >> R version 2.9.0 (2009-04-17)
> >> i486-pc-linux-gnu
> >>
> >> [snip]
> >>
> >>
> > 
> > 
> http://wiki.r-project.org/rwiki/doku.php?id=getting-started:in
> stallation:debian
> > 
> > suggests
> > 
> > (sudo) apt-get install r-base-dev
> 
> Ben,
> 
> Installing r-base-dev was the key.  Thanks!  Now 
> install.packages('quantreg') works perfectly.
> 
> Frank

There are some gotchas buried in the Depends: line for
R-base-core, which all the other R-base* packages depend
upon.  It says it depends on lapack or atlas but installing
libatlas-base-dev does not make a /usr/lib/liblapack.so so
sequence
   aptitude install libatlas-base-dev
   aptitude install r-base-dev
(on a freshly installed Ubuntu) results in Frank's problem 
(fire up R and install.packages("quantreg")
fails because the linker cannot resolve -llapack.
Purging atlas package and reinstalling r-base-dev fixes
things so the desired /usr/lib/lliblapack.so is used.

Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com  

> 
> > 
> > or perhaps
> > 
> > sudo apt-get build-dep r-base
> > 
> > also see
> > 
> > http://cran.r-project.org/bin/linux/ubuntu/
> > 
> > for instructions on access to more up-to-date
> > repositories, the most salient of which are:
> > ====================
> > add
> > 
> >    deb http://<my.favorite.cran.mirror>/bin/linux/ubuntu jaunty/
> > 
> > (or hardy, intrepid, etc.) to /etc/apt/sources.list
> > 
> > The Ubuntu archives on CRAN are signed with the key of 
> "Vincent Goulet
> > <vincent.goulet at act.ulaval.ca>" with key ID E2A11821. You 
> can fetch this key
> > with
> > 
> >    gpg --keyserver subkeys.pgp.net --recv-key E2A11821
> > 
> > and then feed it to apt-key with
> > 
> >    gpg -a --export E2A11821 | sudo apt-key add -
> > 
> > 
> 
> 
> -- 
> Frank E Harrell Jr   Professor and Chair           School of Medicine
>                       Department of Biostatistics   
> Vanderbilt University
>