[R] installing mgcv (Knoppix/Debian unstable)

Tue May 11 18:44:24 CEST 2004

On Tue, May 11, 2004 at 12:28:57PM -0400, Ben Bolker wrote:
> 
>   Didn't know it was there (and it didn't occur to me to look ...).
> 
>   I have installed a few other of the Debianized packages, but I'm fairly
> new to Debian and don't know offhand how to get a list of which packages
> exist in Debian form and what their names are (or how to say "install all
> R packages")

Communicating that is indeed a problem, as is keeping up changes in CRAN (as
I had missed the 1.0.5 of mgcv).  IIRC Doug Bates had recently posted a nice
expression to be run from inside R. I tend to use the shell, so something
like this works (but it still 'misses' goodies like ESS or Ggobi):

edd at homebud:~> apt-cache search "r-" | grep "^r-"
r-base - GNU R statistical computing language and environment
r-base-core - GNU R core of statistical computing language and environment
r-base-dev - GNU R installation of auxiliary GNU R packages
r-base-html - GNU R html docs for statistical computing system functions
r-base-latex - GNU R LaTeX docs for statistical computing system functions
r-cran-abind - GNU R abind multi-dimensional array combination function
r-cran-boot - GNU R package for bootstrapping functions from Davison and Hinkley
r-cran-car - GNU R Companion to Applied Regression by John Fox
r-cran-cluster - GNU R package for cluster analysis by Rousseeuw et al
r-cran-coda - Output analysis and diagnostics for MCMC simulations in R
r-cran-dbi - database interface for R
r-cran-design - GNU R regression modeling strategies tools by Frank Harrell
r-cran-effects - GNU R graphical and tabular effects display for glm models
r-cran-foreign - GNU R package to read / write data from other statistical systems
r-cran-gtkdevice - GNU R Gtk device driver package
r-cran-hmisc - GNU R miscellaneous functions by Frank Harrell
r-cran-its - GNU R package for handling irregular time series
r-cran-kernsmooth - GNU R package for kernel smoothing and density estimation
r-cran-lattice - GNU R package for 'Trellis' graphics
r-cran-lmtest - GNU R package for diagnostic checking in linear models
r-cran-mapdata - GNU R support for producing geographic maps (supplemental data)
r-cran-maps - GNU R support for producing geographic maps
r-cran-mcmcpack - GNU R routines for Markov chain Monte Carlo model estimation
r-cran-mgcv - GNU R package for multiple parameter smoothing estimation
r-cran-multcomp - GNU R package for multiple comparison procedures
r-cran-mvtnorm - GNU R package to compute multivariate Normal and T distributions
r-cran-nlme - GNU R package for (non-)linear mixed effects models
r-cran-qtl - [Biology] GNU R package for genetic marker linkage analysis
r-cran-quadprog - GNU R package for solving quadratic programming problems
r-cran-rcmdr - GNU R platform-independent basic-statistics GUI
r-cran-relimp - GNU R package for inference on relative importance of regressors
r-cran-rgl - GNU R package for three-dimensional visualisation using OpenGL
r-cran-rmysql - MySQL interface for R
r-cran-rodbc - GNU R package for ODBC database access
r-cran-rpart - GNU R package for recursive partitioning and regression trees
r-cran-rquantlib - GNU R package interfacing the QuantLib finance library
r-cran-sm - GNU R package for kernel smoothing methods
r-cran-statdataml - GNU R package for XML-based data exchange
r-cran-survival - GNU R package for survival analysis
r-cran-tkrplot - GNU R embedded Tk plotting device package
r-cran-tseries - GNU R package for time-series analysis and comp. finance
r-cran-vr - GNU R package accompanying the Venables and Ripley book on S
r-cran-xml - An XML package for the R language
r-doc-html - GNU R html manuals for statistical computing system
r-doc-info - GNU R info manuals statistical computing system
r-doc-pdf - GNU R pdf manuals for statistical computing system
r-gnome - GNU R Gnome gui for statistical computing system
r-mathlib - GNU R standalone mathematics library
r-noncran-lindsey - GNU R libraries contributed by Jim and Patrick Lindsey
r-omegahat-rgtk - GNU R binding for Gtk
r-other-gking-zelig - GNU R package providing a unified front-end for estimating statistical models
r-recommended - GNU R collection of recommended packages [metapackage]
r-omegahat-ggobi - GNU R package for the GGobi data visualization system
r-cran-mapproj - GNU R support for cartographic projections of map data
r-cran-cgiwithr - GNU R package for interpretation and creation of web forms
r-cran-cgiwithr-doc - GNU R package CGIwithR - documentation
r-cran-gregmisc - GNU R package with miscellaneous functions by Greg Warnes et al
r-cran-rpvm - GNU R package interfacing PVM libraries for distributed computing
r-cran-rmpi - GNU R package interfacing MPI libraries for distributed computing
r-cran-snow - GNU R package for 'simple network of workstations' dist. computing
edd at homebud:~> 

This list is probably longer than what you'd get on your system as it
contains some local packages not yet in Debian (e.g. pvm, mpi, snow) and
maybe something I did as Debian package sponsoring too ...

We try to be "formal" about the names, so it should be 
	r-cran-$CRANNAME
or
	r-other-$AUTHOR-$NAME    (as with Gary King et al's 'zelig')
but that isn't religiously enforced yet.

Lastly, if you're already based on Knoppix, you could also try using my
Quantian derivative of Knoppix -- it will have most if not all of the above
already installed; see http://dirk.eddelbuettel.com/quantian for details.  

Regards, Dirk

> 
>   cheers,
>     Ben
> 
> On Tue, 11 May 2004, Dirk Eddelbuettel wrote:
> 
> > 
> > Hi Ben,
> > 
> > On Tue, May 11, 2004 at 11:57:40AM -0400, Ben Bolker wrote:
> > > 
> > >   Just in case anyone cares or is hitting the same problem:
> > 
> > Any reason you choose to not install install the evailable package?
> > 
> > edd at chibud:~> apt-cache policy r-cran-mgcv
> > r-cran-mgcv:
> >   Installed: 0.9.6-3
> >   Candidate: 0.9.6-3
> >   Version Table:
> >      1.0.4-1 0
> >          -1 http://basebud unstable/main Packages
> >  *** 0.9.6-3 0
> >         500 http://basebud testing/main Packages
> >         100 /var/lib/dpkg/status
> > edd at chibud:~> 
> > 
> > > to install current mgcv (1.0-5) on 1.9.0 on Knoppix/Debian unstable I had 
> > > to:
> > > 
> > > # cd /usr/lib
> > > # ln -s /usr/lib/atlas/libblas.so.3 libblas-3.so
> > > # ln -s /usr/lib/atlas/liblapack.so.3 liblapack-3.so
> > >
> > > Otherwise compilation couldn't find -lblas-3 or -llapack-3
> > 
> > The R package may need a recompilation if something changed w.r.t. to the
> > libraries, though Camm is typically careful not to require this. I need to
> > check this, unfortunately my main build machine is currently sick.
> >   
> > > (I could have gotten away with the links in /usr/lib/atlas instead of
> > > /usr/lib, as /usr/lib/atlas was listed in /etc/ld.so.conf)
> > 
> > You should never need a fudge like this on Debian system. Something else is
> > not right, and we need to fix that.
> > 
> > Dirk
> > 
> > 
> 
> -- 
> 620B Bartram Hall                            bolker at zoo.ufl.edu
> Zoology Department, University of Florida    http://www.zoo.ufl.edu/bolker
> Box 118525                                   (ph)  352-392-5697
> Gainesville, FL 32611-8525                   (fax) 352-392-3704
> 
> 

-- 
The relationship between the computed price and reality is as yet unknown.  
                                             -- From the pac(8) manual page