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Building R on Mac OS X-"dumping methods" problem

10 messages · Tom Kennedy, Ulises M. Alvarez, Jan de Leeuw +3 more

Tom Kennedy
# 
I have done some more homework.
I am running macos X 10.2.1 on a G3 700MHz ibook.
Developer tool July 2002 with August update.

I get R by rsync. I have tried all three version released, pathched and 
devel and get the same problem with all of them.

If I run nm on methods.so, I get:

       $nm methods.so |grep R_initialize
       00002db8 T _R_initialize_methods_metadata

It is present but, is the leading underscore significant?

There is no 'ldd' on darwin but otool -L is the same I think. It gives 
the same output.

        $otool -L methods.so
        methods.so:
         /usr/local/lib/R/bin/libR.dylib (compatibility version 0.0.0, 
      current version 0.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current 
version 60.2.0)

This is a curious result since there is not currently a library at
/usr/local/lib/R/bin/libR.dylib since I have not install yet.
I did do a partial install and it made no difference.

If I look for libraries in R.bin, I get the following result and it 
looks OK to me. Likewise it is identical for the dynamic library 
libR.dylib. It is finding the dlcompat libdl, using the system ncurses, 
libc and libz library.

$otool -L R.bin
R.bin:
         /System/Library/Frameworks/Carbon.framework/Versions/A/Carbon 
(compatibility version 2.0.0, current version 122.0.0)
         /opt/local/lib/libdl.1.dylib (compatibility version 1.0.0, 
current version 1.0.0)
         /usr/lib/libncurses.5.dylib (compatibility version 5.0.0, 
current version 5.0.0)
         /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, 
current version 60.2.0)
         /usr/lib/libz.1.1.3.dylib (compatibility version 1.0.0, current 
version 1.1.3)

In the R.bin, I looked for Call routine

$nm R.bin|grep Call
00002bd8 T _R_addCallRoutine
00071988 T _R_addTaskCallback
00071624 T _R_getTaskCallbackNames
000715c0 T _R_removeTaskCallback
00071810 T _R_taskCallbackRoutine
000860e8 T _RecordGraphicsCall
000712a4 T _Rf_addTaskCallback
00002c34 T _Rf_freeCallSymbol
000032c8 T _Rf_lookupRegisteredCallSymbol
00071480 T _Rf_removeTaskCallbackByIndex
000713a0 T _Rf_removeTaskCallbackByName
0005544c t _assignCall
00012ccc T _baseCallback
00085038 t _makeErrorCall
0005533c t _replaceCall

Does this look right?

I tested another .Call interface by running R and then loading library 
ctest. ansari uses a library call and I got this result for 
example(ansari.test).

...
Warning message:
Cannot compute exact p-value with ties in: ansari.test.default(ramsay, 
jung.parekh)
Error in .C("pansari", as.integer(length(q)), p = as.double(q), 
as.integer(m),  :
         C/Fortran function name not in load table

Looks like this is not just a problem in metheds.so.
Could the configure process be going wrong? The R.bin seems
to work OK but it cannot load external dynamic libraries.

Regards Tom




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Ulises M. Alvarez
# 
Hi:

Has anybody of the Mac users been able to install R 1.6.0 on a Mac with 
the OS Jaguar?

For what I've been reading, doesn't seem so.

Any help will be appreciated.
Jan de Leeuw
# 
Darwin/X11 R 1.6.0 installs out of the box on Jaguar, provided
you have the appropriate fink libraries on your machine (xfree86,  
dlcompat,
readline, tcltk, libjpeg, libpng, g77 or f2c, gnome if you want it),
and provided g77, readline, and f2c are the 10.2 versions of
these fink tools. So: update the OS, then update fink, then install R.

See ftp://gifi.stat.ucla.edu/pub/R-1.6.0.tar.gz (this has more than
240 precompiled packages), but it does not have the dylibs from
fink (and, for some packages, from various other places).

What you had been reading about was an attempt to use darwinports
instead of fink (so far without success).

Also, the Carbon R runs just fine on Jaguar.
On Sunday, October 20, 2002, at 10:14 AM, Ulises Mora Alvarez 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 at stat.ucla.edu
homepage: http://gifi.stat.ucla.edu
   
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-------------------------
           No matter where you go, there you are. --- Buckaroo Banzai
                    http://gifi.stat.ucla.edu/sounds/nomatter.au
   
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-------------------------

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      David Orlovich
    

    

      
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Initially I had troubles installing the Darwin X11 R but this weekend I  
successfully compiled KDE, then I compiled R 1.6.0 on my machine  
(running Jaguar), and it all works fine.  Don't give up :)  David  
Orlovich.

        
On Monday, October 21, 2002, at 09:43 AM, Jan de Leeuw wrote:

        

            

      
      
      
    

        
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      Ulises M. Alvarez
    

    

      
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I've just tried. It doesn't work.

After running: ./configure
I got:
Error message:
configure: error: Neither an F77 compiler nor f2c found

I've just installed and updated fik and the X server.

I'm doing something wrong. More help would be appreciated.
By the way, how you compiled KDE?

Thanks.

OS: Jaguar 10.2.1
Processor: G3 700 Mhz

        
On Mon, 21 Oct 2002, David Orlovich wrote:

        

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      David Orlovich
    

    

      
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have you got the developer tools installed from developer.apple.com?

        
On Monday, October 21, 2002, at 02:02 PM, Ulises Mora Alvarez wrote:

        

            

      
      
      
    

        
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Send "info", "help", or "[un]subscribe"
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      Don MacQueen
    

    

      
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Type

   fink list | grep ' i '

and look at the results. It should include this:

  i      g77     3.1-20020420-2  GNU FORTRAN77 compiler.

If not, then type

   fink install g77

(and sit back and wait a long time!).

You will have to take similar steps for the other packages from fink 
that Jan mentioned in his earlier response to your questions.

Then try ./configure again.

-Don

        
At 8:02 PM -0500 10/20/02, Ulises Mora Alvarez wrote:

            

      
      
      
    

        
<- snip ->

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    
5 days later

    

      
      

        


  

        

      Ulises M. Alvarez
    

    

      
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Hi:

First, I like to thank you all for the help I've already received.

Second: After successful ./configure & make, How in the world can I 
launch the R software?

I've tried from a terminal, with and without Fink, and with and without 
the X server.

Any help is appreciated.

Version: 1.6.0
OS: Mac OS 10.2.1 Jaguar
Processor: G3 700 MHz

        
On Mon, 21 Oct 2002, Don MacQueen wrote:

        

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Matej Cepl
    

    

      
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On Sat, Oct 26, 2002 at 03:35:12PM -0500, Ulises Mora Alvarez wrote:

            

      
      
      
    

        
You should make probably also 'make install' (see INSTALL file) 
and the program should be put in the right place (whatever it is 
on Jaguar).

Matej

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Matej Cepl
    

    

      
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On Sat, Oct 26, 2002 at 05:36:40PM -0400, Matej Cepl wrote:

            

      
      
      
    

        
Sorry, there's a typo here: it should read "so that the program 
is put in the right place" instead of "and the ..." -- running 
'make install' should secure the trick.

Matej