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

[Chris Evans]

Really odd to know what to say to this Paul, always a challenge to know 
how to mix the personal/human and the technological on techno lists.

Well, I'm way too old to be a boy scout.  I've been using R for about 13 
years I think, S+ before that, SAS and SPSS (ugh) before that.  About 25 
years ago I wrote my own little stats package in dBaseII on a CP/M 
"portable".  I've used Linux, including compiling programs and kernels, 
for about 15 years but I don't pretend to be great programmer.  I'm just 
trying to use update.packages() on top of a main install from the superb 
Ubuntu repositories and don't really understand what's happening.

Next time I'll simply ask:
"Does anyone else try to do this?"
"If so, do you get the same or different results?"
"If different, am I doing something differently or wrongly?"

I'll return to the issues when I get back from a much needed week off!

Thanks to you and all,

C

Paul Johnson sent the following  at 06/08/12 06:06:

>> OK.  Can people help clarify this?
> OK, I can feel myself going into long-winded professor mode. After
> this, I'm done on this topic.
>
> The answer is "its just a matter of taste." What do you think is
> fun/interesting about running Linux and using R?  Did you ever compile
> the Linux kernel?  I have. What an adventure.  Can you write programs?
> Do you want to learn  how? You'll have to compile programs,
> eventually.  But maybe  you aren't interested in that, maybe you just
> want to "use" R and the packages other people prepare, in which case a
> lot of the OS mumbo-jumbo is off to the side. If there is a Debian
> package repository, use it. Your time is better spent at learning to
> use Emacs with ESS to develop R code than it is on compiling the R
> packages that you will use. I think that's almost certainly true. if
> the packages exist on a repository, that is.
>
> If you were an MS Windows user, the chances would be good that you'd
> never have to compile an R package because the CRAN has a setup that
> builds all packages and makes them available for download on Windows.
> If there were only one Linux distribution, I expect they would do it
> for Linux as well. It is possible to compile packages for yourself on
> Windows.  Duncan Murdoch assembled a large collection of compilers and
> other build tools called RTools (see
> http://cran.r-project.org/bin/windows). I installed it a few months
> ago. It is like a tiny collection of all the best Unix/Linux programs
> assembled in a collection for Windows systems. Quite awesome.  I
> suppose, if I used Windows, I'd want t o build my own packages, but
> I'd only do that so I wouldn't feel so much like I was using Windows.
>
> The Debian "official" repositories (or whatever distribution) can't
> possibly stay up to date on 1000s of R packages. They don't even try.
> I don't even try anymore.* They provide deb packages for some R
> packages, maybe 100s of the most likely ones.  Some programmers try to
> help users by providing their own unofficial repositories that include
> more or newer Debian packages of R stuff. That's where the PPA
> archives come into play.  The PPA thing is a Ubuntu terminology, an
> effort to streamline your installation and use of Debian packages that
> are not  yet in the official repository..  Those repositories reflect
> a tremendous amount of work. If you and I decided "we wish package XYZ
> had a Debian version," we could build the package and then host our
> own repository.  Since our packages are from Chris and Paul, and not
> the official Ubuntu team, they aren't in the distribution, but we
> could make them available for people to use.
>
> Should use choose to use the deb packages from whatever repo or should
> you compile your own? As I said in the start of this thread, I'd say
> to my students, "keep fighting, eventually you will learn about how to
> do this and you will be smarter as a result."  A couple of the package
> managers have written that I'm encouraging folks like you to waste
> your time. They say "just use the deb packages. That is what they are
> there for."  I can understand why they feel that way. They went to the
> trouble of building it.
>
> I encourage people to learn to compile packages because I think it is
> fun.  It is educational. You learn about software development. I was a
> "boy scout". Someday, you will want to use an R package for which
> nobody has built a distribution-specific package.  So you might as
> well be prepared for that day and get comfortable with compiling
> things. The Gentoo LInux distribution takes that philosophy to its
> logical conclusion, and it tries to make users re-compile every
> package on their operating system. Not just R-related packages.
> Everything. That's too hardcore for me. The last time I compiled gcc
> took almost a full day.  But, if I were stranded on an island with a
> computer and the gcc source code, I could eventually build a compiler,
> and there's some satisfaction in that.
>
> So find out what you think is fun, and do that :)
>
> pj
>
> * In 2001 or so, the R package repository was small enough that I
> could have my lab PC's build every package and stay up to date. By
> 2003, I noticed that the R package update would start at 5pm and still
> be going when I came for work.  After that, I had to drop my "build
> everything" commitment and started a list of packages I'll always
> install.
>
>
>>
>> Thanks again Paul and John,
>>
>> Chris
>>
>>
>> --
>> Chris Evans <chris at psyctc.org> Skype: chris-psyctc
>> Consultant Psychiatrist in Psychotherapy, Notts. PDD network;
>> Professor, Psychotherapy, Nottingham University
>> *If I am writing from one of those roles, it will be clear. Otherwise*
>> *my views are my own and not representative of those institutions    *
>> If you have difficulty Emailing me on this address or getting a reply,
>> send again but cc to:       chris dot evans at nottshc dot nhs dot uk
>> and to:                     c dot evans at nottingham dot ac dot uk
>>
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>
>


-- 
Chris Evans <chris at psyctc.org> Skype: chris-psyctc
Consultant Psychiatrist in Psychotherapy, Notts. PDD network;
Professor, Psychotherapy, Nottingham University
*If I am writing from one of those roles, it will be clear. Otherwise*
*my views are my own and not representative of those institutions    *
If you have difficulty Emailing me on this address or getting a reply,
send again but cc to:       chris dot evans at nottshc dot nhs dot uk
and to:                     c dot evans at nottingham dot ac dot uk