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Komodo, SciViews-K, and 64 bit R

6 messages · Jonathan Greenberg, Philippe GROSJEAN, David Winsemius +1 more

Original
Jonathan Greenberg
# 
MacRers:

    I've been having a bit of trouble getting SciViews working cleanly 
with R64 (from the AT&T website) -- first off, what is the proper "sudo 
ln -s" statement to get it working with MacOS X?  Secondly, is there any 
way to get Komodo/Sciviews-K to work with "R64.app" besides simply 
renaming that to R.app?

    Thanks!

--j
Philippe GROSJEAN
# 
Hello,

The "ln -s" command you talk about is to make a symbolic link to Komodo 
Edit (its installer fails to do that, despite there are a couple of 
useful command line options provided). Open a terminal window on your 
Mac and type this, providing you installed Komodo Edit.app in 
/Applications (all on one line):

sudo ln -s /Applications/Komodo\ Edit.app/Contents/MacOS/komodo 
/usr/bin/komodo

You will be prompted for administrative password. R can now open 
documents directly inside Komodo.

For your second question, indeed, we should support 64-bit R too, and 
including R64.app and R --arch x86_64/R --arch ppc64. For the moment, 
you can do the changes by yourself like this:

- Open the toolbox in Komodo: View -> Tabs -> Toolbox

- Navigate to SciViews-K/GUI/Menus/R/Start R folder in the toolbox.

- Copy R app (Mac) entry (right-click -> copy in context menu)

- Select 'Start R' folder again and right-click -> paste)

- Select the pasted 'R app (Mac)' entry and right-click -> properties

- In the Properties dialog box, rename it to 'R64 app (Mac)', and in 
Command: change it to 'open -a /Application/R64.app ....'

Restart Komodo Edit. You should be able to connect to your R 64-bit 
application.

P.S.: untested, please report back your results

P.S.2: you should better use the SciViews-Help mailing list 
(http://r-forge.r-project.org/mail/?group_id=194) and/or the feature 
request in the SciViews Tracker 
(http://r-forge.r-project.org/tracker/?group_id=194).

..............................................<?}))><........
  ) ) ) ) )
( ( ( ( (    Prof. Philippe Grosjean
  ) ) ) ) )
( ( ( ( (    Numerical Ecology of Aquatic Systems
  ) ) ) ) )   Mons-Hainaut University, Belgium
( ( ( ( (
..............................................................
Jonathan Greenberg wrote:
David Winsemius
# 
I am getting a error message during an effort to use the Package  
Installer with a source copy of cairoDevice:

* Installing *source* package 'cairoDevice' ...
checking for pkg-config... no
ERROR: Cannot find pkg-config.
ERROR: configuration failed for package 'cairoDevice'
--------
I seem to have pkg-config per locate from the Terminal:

david-winsemiuss-mac-pro:~ davidwinsemius$ locate pkg-config
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/bin/pkg- 
config
/sw/bin/pkg-config
/sw/share/man/man1/pkg-config.1
/usr/X11/share/man/man1/pkg-config.1.gz
/usr/share/zsh/4.3.4/functions/_pkg-config
------
The UNIX Appendix of the Installation Manual (p 29) says: "Mac OS X  
comes with none of these libraries, but cairo support has been added  
to the binary distribution: pkg-config is still needed and can be  
compiled from the sources. "

But that is not particularly helpful to me. Is there some environment  
variable or path has not been defined properly? I tried downloading  
pkgconfig-0.18 but its README file is not sufficiently detailed for my  
level of understanding of the UNIX underbelly of Mac OS X.

 > sessionInfo()
R version 2.8.1 Patched (2009-01-19 r47650)
i386-apple-darwin9.6.0

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets   
methods   base

other attached packages:
[1] Design_2.2-0    survival_2.35-4 Hmisc_3.6-0

loaded via a namespace (and not attached):
[1] cluster_1.12.0  grid_2.8.1      lattice_0.17-25 tools_2.8.1
Warning message:
In install.packages(c("cairoDevice"), lib = "/Library/Frameworks/ 
R.framework/Resources/library/",  :
   installation of package 'cairoDevice' had non-zero exit status
 >

David Winsemius, MD
Heritage Laboratories
West Hartford, CT
Simon Urbanek
#
On Jul 2, 2009, at 10:41 , David Winsemius wrote:

            

      
      
      
    

        
Yes, try

Sys.setenv(PATH=paste("/Library/Frameworks/GTK+.framework/Resources/ 
bin",Sys.getenv("PATH"),sep=":"))

(BTW: I'm not quite sure why you would try to compile it from sources  
- it's available in binary from from CRAN).

Cheers,
Simon

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      David Winsemius
    

    

      
      #
    

  


  

      
On Jul 2, 2009, at 12:42 PM, Simon Urbanek wrote:

        

            

      
      
      
    

        
Thanks. Unfortunately, I now get a huge number of error messages:  
starting with:

trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/cairoDevice_2.10.tar.gz'
Content type 'application/x-gzip' length 39058 bytes (38 Kb)
opened URL
==================================================
downloaded 38 Kb

* Installing *source* package 'cairoDevice' ...
checking for pkg-config... pkg-config
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/ 
Resources/include -I/Library/Frameworks/R.framework/Resources/include/ 
x86_64 -I/Library/Frameworks/GTK+.framework/Versions/2.14.X11/ 
Resources/include/gtk-2.0 -I/Library/Frameworks/GTK+.framework/ 
Versions/2.14.X11/Resources/lib/gtk-2.0/include -I/Library/Frameworks/ 
GTK+.framework/Versions/2.14.X11/Resources/include/atk-1.0 -I/Library/ 
Frameworks/GTK+.framework/Versions/2.14.X11/Resources/include/cairo -I/ 
Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/include/ 
pango-1.0 -I/Library/Frameworks/GTK+.framework/Versions/2.14.X11/ 
Resources/include/glib-2.0 -I/Library/Frameworks/GTK+.framework/ 
Versions/2.14.X11/Resources/lib/glib-2.0/include -I/Library/Frameworks/ 
GTK+.framework/Versions/2.14.X11/Resources/include/pixman-1 -I/Library/ 
Frameworks/GTK+.framework/Versions/2.14.X11/Resources/include/ 
freetype2 -I/Library/Frameworks/GTK+.framework/Versions/2.14.X11/ 
Resources/include -I/Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/libpng12   -g -I/usr/local/include    - 
fPIC  -g -O2 -c cairoDevice.c -o cairoDevice.o
In file included from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib/gtypes.h:34,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib/galloca.h:34,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib.h:32,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gobject/gtype.h:26,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gobject/gboxed.h:26,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib-object.h:25,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/gioenums.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/giotypes.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/gio.h:28,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gdk/gdk.h:32,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gtk/gtk.h:32,
                  from cairoDevice.h:1,
                  from cairoDevice.c:1:
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/lib/ 
glib-2.0/include/glibconfig.h:443:2: error: #error "Unsupported  
architecture"
In file included from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib/galloca.h:34,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib.h:32,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gobject/gtype.h:26,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gobject/gboxed.h:26,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib-object.h:25,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/gioenums.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/giotypes.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/gio.h:28,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gdk/gdk.h:32,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gtk/gtk.h:32,
                  from cairoDevice.h:1,
                  from cairoDevice.c:1:
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/include/ 
glib-2.0/glib/gtypes.h:45: error: expected ?=?, ?,?, ?;?, ?asm? or  
?__attribute__? before ?typedef?
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/include/ 
glib-2.0/glib/gtypes.h:94: error: expected ?=?, ?,?, ?;?, ?asm? or  
?__attribute__? before ?*? token
In file included from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib/galloca.h:34,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib.h:32,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gobject/gtype.h:26,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gobject/gboxed.h:26,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib-object.h:25,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/gioenums.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/giotypes.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gio/gio.h:28,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gdk/gdkapplaunchcontext.h:30,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gdk/gdk.h:32,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/gtk-2.0/gtk/gtk.h:32,
                  from cairoDevice.h:1,
                  from cairoDevice.c:1:
/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/include/ 
glib-2.0/glib/gtypes.h:396:2: error: #error unknown ENDIAN type
In file included from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/glib.h:33,
                  from /Library/Frameworks/GTK+.framework/Versions/ 
2.14.X11/Resources/include/glib-2.0/gobject/gtype.h:26,
------snipped further errors----------

            

      
      
      
    

        
It is and I have cairoDevice 2.9-2 installed, but I got this message  
when I tried to load playwith 0.9-43 when using the 64 bit GUI:

Loading required package: lattice
Loading required package: cairoDevice
Error: package 'cairoDevice' is not installed for 'arch=x86_64'
In addition: Warning message:
In install.packages(c("cairoDevice"), lib = "/Library/Frameworks/ 
R.framework/Resources/library/",  :
   installation of package 'cairoDevice' had non-zero exit status

So I thought I would try to install from source. Wasn't there a time  
in the not too distant past when Mac binary packages in CRAN did not  
support the 64-bit architecture ?

            

      
      
      
    

        
David Winsemius, MD
Heritage Laboratories
West Hartford, CT

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
On Jul 2, 2009, at 13:04 , David Winsemius wrote:

        

            

      
      
      
    

        
Ah, that explains!  Well, the reason why there are no 64-binaries is  
the above (the GTK+ binary you have doesn't support 64-bit) --  
essentially you have to build the whole GTK+ and all dependencies from  
sources for x86_64 in order to use cairoDevice in 64-bit ...

            

      
      
      
    

        
They do (in the Leopard build), but only where the dependencies are  
met. In this case we have to working GTK+ for 64-bit, so they are not  
built.

Cheers,
Simon