[R-sig-Debian] "Debain" way of installing packages

[A.J. Rossini]

YMMV, but what I do is to install duplicates (i.e. R CMD INSTALL
places things in /usr/local/, and apt-get in /usr/), and resolve the
library I want at load time.

This has a few advantages, and the obvious disadvantage that you can
shoot yourself in the foot REALLY EASILY if you don't pay attention to
what you've got configured.

best,
-tony



On 4/24/05, Gorjanc Gregor <Gregor.Gorjanc at bfro.uni-lj.si> wrote:
> Hello!
> 
> I use Debian GNU/Linux at work and I really like apt-get tool. As far as
> I understand the whole picture, there are now some Debian packages of R
> packages. Build of Debian packages is done automagically by Perl script.
> 
> By the way, what is the status of Debianizing R packages? Is it stopped,
> just holded, ... I don't know so I am asking
> There is also Bioconductor and I am aware that the list of packages is
> growing quite fast and afterall I understand that there is probably to
> few people to work on Debianization.
> 
> The main point of this mail is however installation. I usually first
> try to use apt-get install and if there is no Debian package I use
> R tools. However some packages that I have already installed with R tools
> might  eventually appear as Debian packages, ... or I might use
> update.packages() for Debian packages. By the way is field
> 'Package-Manager: Debian' already implemented. I would check, but I
> unfortunately don't have Debain at home.
> 
> I was thinking on some functions or eventually an R package r-debian,
> which would ease this installation dilemma. Actually I wrote something
> already in december but put it off. It is given bellow. It is probably
> far from optimal but it was just a proof of concept. Many more functions
> would be needed to fuzz everything up. Any comments?
> 
> debian.install.packages <- function(package, ...) {
> 
>     # Description:
>     # Installs package on Debian GNU/Linux system. For given R package it
>     # tries to get Debian package and install/upgrade it with apt-get if it
>     # exists.  Otherwise install.packages() is used.
>     # Gregor GORJANC 2004-12-30
> 
>     # Arguments:
>     # package: R package name as character, only one
>     # ...: other parameters for install.packages() or update.packages()
> 
>     # Examples:
>     # debian.install.packages("Design")
> 
>     # Code:
>     # apt-get update i.e. refresh list of Debian packages
>     system(apt-get update)
> 
>     # Transform R package name to Debian package name policy i.e change R
>     # package name to lowercase and test if this Debian package exists
>     # (test1). This could be done without grep, but then it is not possible
>     # to test on exit status, since apt-cache search always returns 0.
>     packagelow <- tolower(package)
>     tmp1 <- c("system(\"apt-cache search ^r- | grep")
>     tmp2 <- c("| awk '{print $1}'\", intern = TRUE\)")
>     tmp3 <- as.expression(paste(tmp1, packagelow, tmp2, "\n"))
>     deb <- eval(parse(file = "", text = tmp3))
> 
>     cat("\nR package:", package, "\n")
>     cat("Corresponding Debian package name:", deb, "\n")
> 
>     # Package install/update or upgrade in apt meaning
>     if (length(deb) != 0) { # Debian package does exist
>         cat("Debian package", deb, "exists: yes\n")
>         cat("Proceeding with apt-get.\n")
> 
>         # apt-get install, which can also be used for package upgrade
>         tmp1 <- c("system(\"apt-get install")
>         tmp2 <- as.expression(paste(tmp1, deb, "\")", "\n"))
>         eval(parse(file = "", text = tmp2))
>     }
>     else { # Debian package doesn't exist or something went wrong in test1
>         cat("Debian package", deb, "exists: no\n")
> #        cat("Proceeding with install/update.packages().\n")
> #        install.update.packages(package, ...)
>         cat("Proceeding with install.packages().\n")
>         install.packages(package, ...)
>     }
> }
> 
> One more thing. Why is r-noncran-lindsey and not r-other-lindsey?
> 
> --
> Lep pozdrav / With regards,
>     Gregor Gorjanc
> 
> ------------------------------------------------------------------------
> University of Ljubljana
> Biotechnical Faculty       URI: http://www.bfro.uni-lj.si/MR/ggorjan
> Zootechnical Department    email: gregor.gorjanc <at> bfro.uni-lj.si
> Groblje 3                  tel: +386 (0)1 72 17 861
> SI-1230 Domzale            fax: +386 (0)1 72 17 888
> Slovenia
> 
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> 


-- 
best,
-tony

"Commit early,commit often, and commit in a repository from which we can easily
roll-back your mistakes" (AJR, 4Jan05).

A.J. Rossini
blindglobe at gmail.com