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R version on gifi

12 messages · Jan de Leeuw, Thomas Lumley, A.J. Rossini +3 more

#
Pretty soon, hopefully, the RAqua version will make the Darwin/X11
version unnecessary. In the meantime, for convergence, I'll modify the  
Gifi
version in various ways.

-- It's 1.7.1
-- It no longer supports gnome
-- It still uses Tcl/Tk for X11 (using 8.5 from CVS)
!!  It no longer uses anything from fink (readline and dlcompat
     as on Stefano's site, jpeg and png and teTeX from Gerben Wierda's
     i-installer, Tcl/Tk from cvs, X11 from Apple)
-- the package installer will put everything in /usr/local

This means that all references to /sw in configure.ac can go. This
next distribution will appear probably on wednesday. Undoubtedly
some packages will break, because they still use stuff from /sw,
but I'll fix those as we go along.
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
Editor: Journal of Multivariate Analysis, Journal of Statistical  
Software
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550;  fax (310)-206-5658;  email: deleeuw@stat.ucla.edu
homepage: http://gifi.stat.ucla.edu
   
------------------------------------------------------------------------ 
-------------------------
           No matter where you go, there you are. --- Buckaroo Banzai
                    http://gifi.stat.ucla.edu/sounds/nomatter.au
#
Couple of questions...

Thanks
-Don
At 10:00 AM -0700 6/16/03, Jan de Leeuw wrote:
Is the user expected to have separately installed any or all of these 
various libraries, or are they included in the R distribution and 
installed by the R installer? Or what?

Specifically for X11, does it assume the user has separately 
installed Apple's X11 and QuartzWM, and if so, is it in any way 
dependent on anything unique to Apple's X11? That is, will it work if 
the user is using XFree86/XDarwin and some (any) other window manager?
Do you mean that at some point in the future you intend that the 
configure.ac in the source distribution will remove all references to 
/sw? I'm not sure this is a good idea; I think I would prefer to have 
the option of building from sources using fink for those other things 
(readline, jpeg, png, tetex, etc) if I want to. Otherwise I have to 
learn how to get them from several other sites, increasing my system 
maintenance load and making it harder to keep them up to date.

Can you give specific and substantive reasons why fink should be avoided?

I get the impression that R for OS X is being moved away from being 
another unix R variant (in the sense that Solaris, various Linuxes, 
SGI, etc. are unix variants), and moved toward being a specialized 
platform-specific version. Assuming my impression is more or less 
correct, I'd like to understand the pros and cons of this move.

  
    
#
On Mon, 16 Jun 2003, Don MacQueen wrote:
I think the move is to stop *assuming* fink, not to forbid it.

There are at least two goals

1. To produce a binary OS X distribution for people who don't want to
learn Unix, including an (optional) GUI and an (optional) quartz() device
driver.  If you want to stick with a command line and x11(), you're
welcome to. If you want to compile from sources yourself you can competely
ignore the binary distribution. This binary can't install
anything in /sw (because that would clobber fink) and doesn't want to
assume that anything is already there.


2. To produce a simple minimal set of instructions and dependencies for
compiling R on Mac OS X. A set of instructions that includes installing
fink is (I fervently hope) not minimal.  Of course, if you already have
fink installed you can easily use it to get all the necessary software.

You might in future have to specify a configure option to get configure to
look in /sw for system libraries, but this makes it more similar to other
Unices, not less similar.


	-thomas
#
Standard Apple stuff (such as anything in /usr, including X11) will
not be included in the installer package, but everything needed in  
/usr/local
will

I assume it will work with XFree86/XDarwin and with OroborosX, but
I am not going to test it with those, because I don't use them anymore.

I am sure that if more people want /sw, then it will just stay in. I am
just saying that as far as my distribution (and Stefano's) are concerned
it is not needed any more.

Of course you can always use it if you want to by setting LDFLAGS.

I try to avoid fink because it is a maze of nasty dependencies between
packages, which we do not need for R. It is also very inconvenient
and potentially disastrous to have duplicates of binaries and dynamic
libs in /sw and /usr/local and /usr. For instance, when Apple added
ncurses, many things went wrong. Fink is getting more and more
system-foo packages to deal with cases in which there are alternative
installs, and this will obviously become worse over time as more and
more gets added to Darwin. So (a) from the point of view of R
fink is overkill, and (b) fink has been great to have around for three
years but it is reaching the end of its usefulness period. Only my
opinion, of course.

Your impression that R is moved away from "just another Unix
variant" is correct only insofar as RAqua is being added as another
GUI. All the other GUIs (Terminal, Tcl/Tk, XTerm) remain available,
and for those savvy enough to build R fink and gnome can still be
used. There will just be no binaries.

--- Jan
On Monday, Jun 16, 2003, at 11:45 US/Pacific, Don MacQueen wrote:

            
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
Editor: Journal of Multivariate Analysis, Journal of Statistical  
Software
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550;  fax (310)-206-5658;  email: deleeuw@stat.ucla.edu
homepage: http://gifi.stat.ucla.edu
   
------------------------------------------------------------------------ 
-------------------------
           No matter where you go, there you are. --- Buckaroo Banzai
                    http://gifi.stat.ucla.edu/sounds/nomatter.au
#
On Monday, June 16, 2003, at 08:45 PM, Don MacQueen wrote:

            
The really native version doesn't really need to depend on X11 anymore 
since the use of X11 on Mac OS X was meant for applications that are 
not properly ported to OS X yet. Once Quartz and RAqua are complete 
there is no need for X11.
Jan already listed the main technical reasons why it is indeed a very 
good idea. Apart from that, fink is not an official package and was 
only meant as a temporary solution for people who need a (no matter how 
ugly) way to run existing unix programs on OS X. Hardly any real OS X 
user has installed fink (especially since Jaguar is out). Fink was 
great during the first couple of months when native OS X ports were 
hardly existent, but is now obsolete for mainstream OS X use.
It is not a "move" of R. Mac OS X is simply not "another unix variant". 
Darwin is indeed, but Mac OS X is not. You can compile X11 for Darwin 
and use it exactly the way you can use Linux on a PPC hardware. But Mac 
OS X has many very nice (often proprietary) layers that are important 
to the Mac users, but that part of OS X is not "unix". The goal here is 
to release R which fits in the philosophy of the system - ease of use, 
good integration with the existing frameworks, appealing design. These 
are not properties of unix, but of OS X. So what we need is in fact 
Mac-OS-X-like look and feel. The fact that OS X is unix-based helps 
with respect to the R engine itself - we need no special ports of 
packages anymore, but it has a totally different GUI.

Fortunately R makes a distinction between GUI and the engine, therefore 
we can create a real OS X GUI without affecting other platforms - 
including Darwin ;). "Unix" users are used to compile their own 
software, therefore moving fink support to the category 'optional' is 
only logical, since you can still easily enable it with configure 
parameters and/or environment settings. Real Mac OS X users are used to 
nice, binary distributions, therefore we cannot assume fink and we need 
Quartz device and RAqua. It will be a big help for most OS X users. 
(BTW: no Mac users I know (non-developers) have installed X11.)

Therefore the recent changes are IMHO really important from Mac OS X 
user's view - so far most binaries were rather experimental and assumed 
some unix knowledge (note: there was is no official OS X binary!). It 
was ok to use fink for those as a temporary solution, but the official 
binary cannot rely on unsupported non-Apple packages. The only thing 
external part we really need is libdl and I'm sure we can supply it 
simply with R - such as pcre etc., all other libraries are optional.

Cheers,

Simon

---
Simon Urbanek
Department of computer oriented statistics and data analysis
University of Augsburg
Universit?tsstr. 14
86135 Augsburg
Germany

Tel: +49-821-598-2236
Fax: +49-821-598-2200

Simon.Urbanek@Math.Uni-Augsburg.de
http://simon.urbanek.info
#
Simon Urbanek <Simon.Urbanek@math.uni-augsburg.de> writes:
I think completely agree with Simon here.  MacOSX is great for folks
that like the good things in life, but for chumps who just want a Unix
variant, run a PPC Unix (linux or *bsd or the like).  There are just
enough differences to create user-interface stress, depending on the
particular system configuration...

(of course, I'm one of those who has been using a unix variant for
almost 20 years now, and with the onset of senility, that isn't going
to change).

best,
-tony
#
I appreciate the extra explanations from Simon, Jan, Thomas, and 
Tony. All in all, after having read what you all have to say, the 
things that I found potentially alarming in Jan's message yesterday 
are not so alarming anymore.

-Don
At 2:33 PM +0200 6/17/03, Simon Urbanek wrote:
Except for one major flaw in Aqua--the absence of "focus follows 
mouse", as it is sometimes called in an X Windows context. I consider 
the absence a flaw because I find it incredibly useful to be able to 
type R commands into a window that is partially covered by another 
(usually graphics device) window. This is, of course, a (strongly 
held) personal preference, and I'm well aware that many do not 
consider this to be an issue. The Mac OS has always had this 
limitation, and probably always will, so there's nothing to be done 
about it.

More generally, having RAqua, a version of R that is as "Mac-like" as 
possible, is a good thing; I have co-workers who are more likely to 
use such a version of R. As someone who likes OS X a lot, I like 
anything that promotes it, and a good R gui will do that around here.
Jan cited "Gerben Wierda's i-installer" as a source for jpeg, png, 
and teTex. This source is somehow more "official" than fink? But, 
considering what Jan says, i.e. "everything needed in /usr/local 
will" be included with the installer package, it doesn't matter to 
the end user.
I'm glad to hear that, but when Jan says "all references to /sw in 
configure.ac can go" I do tend to wonder whether that is actually the 
case.
I subscribe to Apples "scitech" mailing list, for people interested 
in using the Mac in scientific applications. I'd say X windows is 
pretty common among those folks. Don't know how many of them would 
consider themselves "developers."

  
    
#
At 6:27 AM -0700 6/17/03, A.J. Rossini wrote:
Then there are those of us who "want it all", by which I mean both 
the goodness of native OS X (desktop apps and all), and _also_ the 
unix side, in a single box.
Make it 15 years for me...

  
    
#
For the chumps:

If you just want a Unix variant, run Darwin. If you just want a Linux
variant, run PPC Linux.
On Tuesday, Jun 17, 2003, at 06:27 US/Pacific, A.J. Rossini wrote:

            
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
Editor: Journal of Multivariate Analysis, Journal of Statistical  
Software
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550;  fax (310)-206-5658;  email: deleeuw@stat.ucla.edu
homepage: http://gifi.stat.ucla.edu
   
------------------------------------------------------------------------ 
-------------------------
           No matter where you go, there you are. --- Buckaroo Banzai
                    http://gifi.stat.ucla.edu/sounds/nomatter.au
#
On Tuesday, June 17, 2003, at 05:11 PM, Don MacQueen wrote:

            
Yes, this is indeed a very nice feature (I've been using it on unix all 
time), but it can be disastrous at the same time. MS Windows has an 
undocumented registry key which allows you to enable this, but once you 
do that you'll realize that a lot of applications assume 
'topmost-has-focus' state and are almost unusable if the 
'focus-follows-mouse' is enabled (example: if you have a mouse over a 
toolbar your document window is inactive - most applications can't deal 
with that). I'm not sure about this in OS X (since we can't really test 
it ;P), but something similar might happen.
Exactly, that's the point :) We don't want to assume things that are 
non-standard. We should provide them if necessary.

There is still one issue to consider in this context: source packages. 
A really 'plain' Mac OS X can't be used to install source packages 
as-is, basically because there are three missing things: Dev Tools, g77 
and latex. The first one is official, so we could require that (and 
probably have to). G77 is really just a few files, so the installer 
could add it if necessary, but I'm not sure about latex. Is building 
packages w/o latex documentation an option? The direct use of source 
packages seems to me as the greatest benefit of OSX being unix-based, 
therefore i wouldn't like to miss it, even if I was pure Mac user...

Cheers,
Simon

---
Simon Urbanek
Department of computer oriented statistics and data analysis
University of Augsburg
Universit?tsstr. 14
86135 Augsburg
Germany

Tel: +49-821-598-2236
Fax: +49-821-598-2200

Simon.Urbanek@Math.Uni-Augsburg.de
http://simon.urbanek.info
#
On Tue, 17 Jun 2003, Simon Urbanek wrote:

            
It's a documented part of TweakUI, and I find it very usable.  After all, 
it I have my mouse over something on the toolbar, I have deliberately
moved focus there (just as in CDE), and it is very natural to someone
used to this from a good Unix windows manager.  Only a very few 
applications cause me problems (most notably the Visual Basic IDE).
It could be.  Checking them is not, though.
At DSC we seemed to decide that we would need a binary packages mechanism 
for the GUI MacOS X port.  I suspect you underestimate the difficulties 
(or overestimate the abilities of the users concerned): the Windows
experience is that is hard to overestimate the ability of the users to 
make stupid errors and not realize what.


As for this being `just another unix version': if only!  Simple things on
any other unix-alike like making a Rlapack dynamic library became major
headaches on darwin, only, and that is still not fully resolved.
#
At 5:45 PM +0200 6/17/03, Simon Urbanek wrote:
For an OS X user with no unix background, I would think that pdf is 
the preferred format, and sufficient.