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

[Douglas Bates]

On Thu, May 29, 2008 at 5:10 PM, Tony Plate <tplate at acm.org> wrote:
> [moving this to R-sig-debian]

> 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.
> (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:

> (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?
> (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?

At the risk of confusing the issue further, I prefer to use "wajig"
which provides a unified command-line interface to apt-get, dselect
and all the other command line tools.  The first package that I
install on a Debian/Ubuntu system is wajig then I use that to do all
the other package maintenance.  It adds command completion and package
name completion for itself to the standard shell completions so I find
it more convenient to use than any GUI like aptitude or synaptic.

Although I would have written to the list what Dirk wrote about

apt-get build-depend r-base

(and I had started to create the message when Dirk's message arrived)
I would actually have used

wajig bui<tab>-<tab> r-base

to install the build-depend packages for r-base.  Then I would have
had to have checked which of the basic tools wajig calls to do the
build-depend installation.  The name wajig indicates that it is a jig
or wrapper around several other package-management functions.  It has
gotten to the point that I don't know which of the basic tools does
what (is it apt-get or dpkg or dpkg-deb or ...?) any more because I
always use wajig, which is even smart enough to prompt you for your
password and get sudo permission for you when you need it.  How many
times have you typed

apt-get install foo

only to realize that you should have typed

sudo apt-get install foo


Because wajig is so flexible it has an incredible number of possible
commands (see the output from

wajig com<tab>

but the basic commands are fast to learn.  I depend on

wajig search "expression"

to find suitable packages and

wajig install pkg_name

to install them.  Other variations include installr, installs and
installrs to install the package plus its recommended or the package
plus its suggested or the package plus its recommended and suggested
packages.

One of the first things I do when I log on to a computer at home or at
the office is to spring up a terminal and run

wajig daily-upgrade

which updates the list of packages and installs any upgrades.

I learned about wajig from Dirk and now use it exclusively.  Do you
still use it, Dirk?

I suppose that younger generations of users will not find it as
convenient as those of us who grew up with command-line interfaces
(and dial telephones that were bolted to the wall and had the handset
attached by a cord) but we older types think it's just groovy.

> (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 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 would say that those are better deleted but I will defer to Dirk if
he says it is advisable to retain those flags.  I don't use those
flags myself and the configure script has no trouble finding the
include files there.

You can find out exactly what configure call Dirk uses to build the
Debian packages by running

wajig build-depend r-base
wajig build r-base

The latter takes a while.


> (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
>>
>
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