[R-sig-Debian] Problem updating packages in 2.15.1 on Ubuntu 12.04: updating options

[Chris Evans]

Thanks Michael, thanks all.  I'm away for a week or so and have been 
buried in my clinical job but when I return I'll pick things up and look 
in detail at your very helpful information and I'll summarise back to 
the list and perhaps try to draft something about the options from a 
relative luser perspective that might be helpful.

Very best all,

Chris

Michael Rutter sent the following  at 05/08/12 20:58:
>
>
> On 08/03/2012 11:16 AM, Chris Evans wrote:
>
> -- Lines deleted --
>
>>> I know for sure from previous debates here that the Debian packagers
>>> expect you to use the packages they provide, and they don't think
>>> "ordinary" users should bother trying to compile packages.
>>
>> OK.  Is that true packagers?  I've had that impression at times but at
>> other times it has also seemed that the packaging is designed to sit
>> alongside the CRAN repositories simply making it much easier to get the
>> bases of a minimal or a really nearly complete R system easily through
>> the Debian or Ubuntu upgrade systems. However, when I find I'm reading
>> things that way I find myself believing that update.packages() ought to
>> remain a non-deprecated option.
>
> I have been at the Joint Statistical Meetings/family vacation, so I am
> finally catching up on this thread and will comment on a couple of things.
>
> I can't speak for Dirk on the Debian side, but the statement "they don't
> think 'ordinary' users should bother trying to compile packages." in
> regards to Ubuntu is absurd in my opinion.  First of all, we supply the
> package r-base-dev, whose description includes "This package ensures
> that other Debian packages needed for installation of some auxiliary R
> packages are installed."  There are ~4000 packages in CRAN, plus others
> on BIOC, Rforge, and other places.  We cannot provide Ubuntu specific
> .debs for all of those packages, so we supply the tools to install them
> from within R.  I assume that anyone that uses R on a regular basis will
> at some point use install.packages from within R due to the fact we
> cannot supply everything as a .deb.
>
> Unfortunately, not all packages build easily within R due to specific,
> non-R libraries that are required.  Sometimes the Ubuntu packages that
> supply those libraries are already installed and the user will never
> know that they were needed, other times a user will need to sort through
> the output of "install.packages" to see what is missing and find the
> required Ubuntu package that will satisfy the dependency.  Ubuntu
> package search (http://packages.ubuntu.com/), Google, and this mailing
> list are excellent resources to help determine what packages is needed.
>
> R based packages (r-base, r-cran-*, and r-bioc-*) are provided for two
> reasons, in my opinion.  One is to make installation easy for end users
> of R using Ubuntu.  By installing r-base, there is no need to worry
> about what compilers, latex engines, libraries, and all the other parts
> that are needed to compile R.  Same goes for r-cran and r-bioc packages.
> The other reason is that we provide updates to users as part of the
> regular updating Ubuntu process.  Not only are users provided with up to
> date versions of R and certain R packages without needing to follow a
> number of mailing lists, the packages have all the Ubuntu specific
> bugs/issues worked out, if there are any.  You don't have to download
> the source and compile Firefox every time Firefox is updated, so why
> should you have to do that for R?
>
> We also design the R packages to work in a specific way.  So, if you
> install R in the default location and either install the available R deb
> packages with apt/synaptic, or install from within R with
> 'install.packages' in the default locations, R *should* work without
> issue.  If it doesn't and the issue can be repeated on a default
> installation, Dirk and I will work to resolve those issues.  If you
> decide to install things in different locations, then we can't guarantee
> that things will always work they way they are supposed to (it also
> become harder to suggest solutions, since we can't recreate the
> problem).  I never have a problem with package locations if I use
> apt/synaptic to install what is available in Ubuntu and 'sudo R' to
> install and update packages from within R, all using the default
> settings.  I always make sure my Ubuntu system is current before I
> update.packages within R, and I have never had an issue with an
> apt/synaptic installed package being updated from within R via
> "update.packages" and not working.
>
> A hint:  Either always install and update packages using R as root (via
> sudo) or install and update packages using user (non-sudo) privileges.
> If you install package via sudo (using install.packages or
> apt/synaptic), update.packages under normal user privileges will not
> allow the update to occur.
>
> It should be pointed out that we assume that the R user has access to
> sudo to install Ubuntu packages via .deb pacakges.  If you do not, than
> you need to work things out with your IT people how to best handle the
> installation and updating of R.
>
>>> That does not speak to the fact that you may not have access to an
>>> up-to-date repository for packages for your particular system.  John
>>> Nash pointed you at one that will work for you.
>>
>> OK.  Let's see if I've got this right or wrong.  I think there are three
>> repositories that a Ubuntu system can use to update R:
>
> Here is a link to some information of the available R repositories for
> Ubuntu:
>
> http://www.personal.psu.edu/mar36/blogs/the_ubuntu_r_blog/installing-r.html
>
> In addition, if you would like access to more than 1100 other R packages
> for Ubuntu, you can use my c2d4u PPA on launchpad.  More details here:
>
> http://www.personal.psu.edu/mar36/blogs/the_ubuntu_r_blog/cran2deb4ubuntu.html
>
>
> I see two main issues with using R on Ubuntu currently.
>
> 1. Documentation.  I need to document things better.  To help with this,
> I have created "The Ubuntu R Blog".  I need to start feeding content to
> R-bloggers and adding more documentation.  It can be found here:
>
> http://tiny.cc/ubunturblog or
> http://www.personal.psu.edu/mar36/blogs/the_ubuntu_r_blog/cran2deb4ubuntu.html
>
>
> 2. install.packages("foo") needs to check to see if the package is
> available in an Ubuntu repository and use that instead of building from
> CRAN.  I have had a couple of people from UseR conferences suggest some
> solutions to this, and I need to sit down and create an Ubuntu specific
> R package to solve this problem.  I will keep you posted on this.
>
> Michael


-- 
Chris Evans <chris at psyctc.org> Skype: chris-psyctc
Consultant Psychiatrist in Psychotherapy, Notts. PDD network;
Professor, Psychotherapy, Nottingham University
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