[R-sig-Debian] [R] need help for building R in Ubuntu 8.04

Dirk Eddelbuettel edd at debian.org
Fri May 30 02:19:20 CEST 2008

Hi Tony,

On 29 May 2008 at 16:10, Tony Plate wrote:
| [moving this to R-sig-debian]

Good move!  Thanks also to everybody for the follow-ups.  As wajig maintainer
and hence initial Debian user,  I fully concur with what Doug said in its
favour. Also note that wajig's author is now also a prolific R/CRAN author
and will keynote at Use R. Small world. Lastly, to add to Tyler's mail, wajig
does in fact call apt-get, aptitude, dselect, dpkg, apt-cache --- $whatever
needed -- to get the job done from _one single interface_.  Very useful.
| Dirk, thanks for this info.
| The r-wiki 
| http://wiki.r-project.org/rwiki/doku.php?id=getting-started:installation:debian 
| contained some slightly different suggestions, but I 
| strongly suspect your suggestions are likely to be better.
| So, I edited (minimally) the r-wiki to add your suggestions.

I saw that as I follow the RSS aggregator at http://planetr.stderr.org which,
among other things, sucks in changes from the R Wiki. So three cheers to you
for enhancing the wiki pages. Right approach!

| (1) added a link to 
| http://cran.r-project.org/bin/linux/ubuntu/ (and debian)
|   saying "look there first"
| (2) added your 3 "apt-get install/build-dep" commands
| I suspect more could be changed (i.e., deleting some 
| unnecessarily complex advice), but first I wanted to try to 
| get answers on two issues:

Agreed. I glanced at the page but was too pressed for time to fix anything.
| (1) The R-wiki recommends "aptitude" over "apt-get" (saying 
| "Debian is well known for its apt-get command to install and 
| update Debian packages. There is also aptitude, which is a 
| bit better in handling dependencies etc.")  Is there any 
| reason to prefer one over the other? 

They are interchangeable. What matters is the internal representation. To
that end, even 'apt' is a layer on top of dpkg, and there are more layers.
Choice is a good thing, not unlike the gazillion different ways in which we
can get the same or similar things done in R :-)

| (http://www.pthree.org/2007/08/12/aptitude-vs-apt-get/ ?) Is 
| it generally OK to mix usage of the two on the same system? 
| (and synaptic too?)  Do the two have the same/similar 
| arguments and syntax?

Wajig smoothes everything. I never use aptitude directly, swore off dselect
many many years ago and mostly just use wajig.
| (2) The R-wiki page suggests commands that seem designed to 
| get around problems that might have been avoided had 
| 'apt-get build-deps r-base' been used (e.g., './configure 
| --x-includes=/usr/include/X11' " x-includes=/usr/include/X11 

Yeah, the x11 thing looks strange. I never needed that.  Note that the
principal author (Kurt) of R's configure logic works on a Debian system so
that just tends to work. GG must have tried this just when xorg stuff was

| was needed as configure script could not find header 
| files.") Are these things better deleted from the Wiki page, 
| or are they sometime necessary even in systems that have 
| been correctly configured?

I'd remove'em or comment'em out. But some gentle testing may be best.

Cheers, Dirk
| (And I'm happy to leave these suggestions alone too, but I 
| know that when I've got suggestions from Dirk re Ubuntu, 
| they've worked for me, and I've been able to drop the more 
| complex fudgy stuff.)
| -- Tony Plate
| Dirk Eddelbuettel wrote:
| > On Wed, May 28, 2008 at 02:29:10PM +0200, Martin Maechler wrote:
| >>>>>>> "EH" == Erin Hodgess <erinm.hodgess at gmail.com>
| >>>>>>>     on Sun, 25 May 2008 13:27:04 -0500 writes:
| >>     EH> Try: ./configure --with-x=no
| >>
| >> well......  no!  really don't.
| > 
| > Seconded. 
| > 
| > At best this qualified for the 'then do not do it' school of advice to the 'it hurts when I do this'.
| > But it truly missed the underlying issue. See below.
| > 
| >> If you want to enjoy a Linux system and building from the
| >> source, and then maybe learn how that is happening, learning
| >> about shell scripts and 'make' and ...
| >> then rather do get the extra ubuntu packages needed.
| > 
| > Or if you 'just' want to run it, install Ubuntu and learn to take
| > advantage of the work of others.
| > 
| >> The advice (below) to get the 'xorg-dev'
| >> is definitely good advice. I have it on the list of packages
| >> I'd always want to install in addition to the basic
| >> ubuntu/debian list.
| >>
| >> But you most probably will find that you need a few more tools /
| >> libraries / headers for your ubuntu system such that you can
| >> build R with all the bells and whistles possible.
| >>
| >> There's the Debian (and "hence" Ubuntu) package
| >> 'r-base-dev'
| >> which contains 'r-base' (i.e. a *binary* version of R; the one
| >> Dirk Eddelbuettel mentioned),
| >> but also most of the compilers/libraries/... that you'd want to
| >> build R from the sources.
| > 
| > Just to be a bit more precise:
| > 
| > i)   'apt-get install r-base' will get you r-base-core and all the
| >      recommended packages --- use this if you want to _run_ R
| > 
| > ii)  'apt-get install r-base-dev' will get all the common header files, 
| >      as well as r-base-core use this if you _also want to build /
| >      install R packages_ incl from CRAN
| > 
| > iii) 'apt-get build-dep r-base' will get you _build dependencies_ for
| >      R and is probably what Martin wanted here.
| > 
| >> Last time I did get 'r-base-dev' on a "virgin" ubuntu system,
| >> I vaguely remember that it did not contain *really* all the
| >> tools I'd wanted, but almost all.
| > 
| > Bug reports are always welcome and a more constructive form of moving
| > things forward than an off-hand comment here :-) Note that I tend not
| > to get the ones filed against Ubuntu so file against Debian please.
| > 
| >> e.g., you may also want the two packages
| >>
| >>   tcl8.4-dev
| >>   tk8.4-dev
| > 
| > Just curious: what did you need them for ? In case you wanted to build
| > R, see iii) above as a possibly more focussed way to get there.
| > 
| > Dirk
| > 

Three out of two people have difficulties with fractions.

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