[R-sig-Debian] [R] need help for building R in Ubuntu 8.04
Martin Maechler
maechler at stat.math.ethz.ch
Fri May 30 09:18:34 CEST 2008
Thanks a lot, Doug and Dirk,
for 'wajig'.
I didn't know it but now plan to use it as well.
One thing though (wajig or apt-get or aptitude):
apt-get build-dep r-base
has a bit a seemingly undesired effect on my ubuntu 8.04 system:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
atlas3-base-dev atlas3-headers r-base-dev refblas3-dev
The following NEW packages will be installed:
debhelper gettext html2text intltool-debian libblas-dev po-debconf
0 upgraded, 6 newly installed, 4 to remove and 83 not upgraded.
2 not fully installed or removed.
Need to get 3181kB of archives.
After this operation, 28.3MB disk space will be freed.
Do you want to continue [Y/n]?
I really don't think I'd want to remove r-base-dev and its
dependencies just because I want to get the remaining tools for
building R (r-base) from the sources.
Is there still a misunderstanding (on my side) ?
Martin
>>>>> "DB" == Douglas Bates <bates at stat.wisc.edu>
>>>>> on Thu, 29 May 2008 18:27:25 -0500 writes:
DB> 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?
DB> At the risk of confusing the issue further, I prefer to use "wajig"
DB> which provides a unified command-line interface to apt-get, dselect
DB> and all the other command line tools. The first package that I
DB> install on a Debian/Ubuntu system is wajig then I use that to do all
DB> the other package maintenance. It adds command completion and package
DB> name completion for itself to the standard shell completions so I find
DB> it more convenient to use than any GUI like aptitude or synaptic.
DB> Although I would have written to the list what Dirk wrote about
DB> apt-get build-depend r-base
DB> (and I had started to create the message when Dirk's message arrived)
DB> I would actually have used
DB> wajig bui<tab>-<tab> r-base
DB> to install the build-depend packages for r-base. Then I would have
DB> had to have checked which of the basic tools wajig calls to do the
DB> build-depend installation. The name wajig indicates that it is a jig
DB> or wrapper around several other package-management functions. It has
DB> gotten to the point that I don't know which of the basic tools does
DB> what (is it apt-get or dpkg or dpkg-deb or ...?) any more because I
DB> always use wajig, which is even smart enough to prompt you for your
DB> password and get sudo permission for you when you need it. How many
DB> times have you typed
DB> apt-get install foo
DB> only to realize that you should have typed
DB> sudo apt-get install foo
DB> Because wajig is so flexible it has an incredible number of possible
DB> commands (see the output from
DB> wajig com<tab>
DB> but the basic commands are fast to learn. I depend on
DB> wajig search "expression"
DB> to find suitable packages and
DB> wajig install pkg_name
DB> to install them. Other variations include installr, installs and
DB> installrs to install the package plus its recommended or the package
DB> plus its suggested or the package plus its recommended and suggested
DB> packages.
DB> One of the first things I do when I log on to a computer at home or at
DB> the office is to spring up a terminal and run
DB> wajig daily-upgrade
DB> which updates the list of packages and installs any upgrades.
DB> I learned about wajig from Dirk and now use it exclusively. Do you
DB> still use it, Dirk?
DB> I suppose that younger generations of users will not find it as
DB> convenient as those of us who grew up with command-line interfaces
DB> (and dial telephones that were bolted to the wall and had the handset
DB> 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?
DB> I would say that those are better deleted but I will defer to Dirk if
DB> he says it is advisable to retain those flags. I don't use those
DB> flags myself and the configure script has no trouble finding the
DB> include files there.
DB> You can find out exactly what configure call Dirk uses to build the
DB> Debian packages by running
DB> wajig build-depend r-base
DB> wajig build r-base
DB> 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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