[R-SIG-Mac] X11 missing? ... was Re: [R] rgl persp3d bounding box color problem.

Prof Brian Ripley ripley at stats.ox.ac.uk
Wed Mar 4 08:53:39 CET 2009 

On Tue, 3 Mar 2009, Rob Goedman wrote:

> David,
>
> I did notice in your log.txt file the following message:
>
> 	ld warning: in /usr/local/lib/libfreetype.dylib, missing required 
> architecture x86_64 in file

And that is the problem.  Simon supplies a libfreetype.a that has

tystie% file /usr/local/lib/libfreetype.a
/usr/local/lib/libfreetype.a: Mach-O universal binary with 4 
architectures
/usr/local/lib/libfreetype.a (for architecture i386):	current ar 
archive random library
/usr/local/lib/libfreetype.a (for architecture ppc):	current ar 
archive random library
/usr/local/lib/libfreetype.a (for architecture x86_64):	current ar 
archive random library
/usr/local/lib/libfreetype.a (for architecture ppc64):	current ar 
archive random library

as part of devpack4-darwin8-bin4.tar.gz (on 
http://cran.r-project.org/bin/macosx/tools/).

I don't have a libfreetype.dylib, and for anyone who wants to 
distribute packages you do want to link statically.  So if you move 
libfreetype.dylib out of the way (and have devpack4 installed), you 
should get a statically linked build and a loadable package.

I'm not going to try to track down the path issues further: if I add 
/usr/X11/bin to the path in R.app, rgl works for me.  So it must some 
aspect of the R.app environment for others.  For the record

> Sys.getenv("PATH")
                                                        PATH
"/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin"
> install.packages("rgl", type="source")
Warning in install.packages("rgl", type = "source") :
   argument 'lib' is missing: using '/Users/ripley/R/Library'
trying URL 'http://cran.r-project.org/src/contrib/rgl_0.83-3.tar.gz'
Content type 'application/x-gzip' length 1653379 bytes (1.6 Mb)
opened URL
==================================================
downloaded 1.6 Mb

* Installing *source* package 'rgl' ...
checking for gcc... gcc -arch i386 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... 
none needed
checking how to run the C preprocessor... gcc -arch i386 -std=gnu99 -E
checking for gcc... (cached) gcc -arch i386 -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... (cached) yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... 
(cached) none needed
checking for libpng-config... yes
configure: using libpng-config
configure: using libpng dynamic linkage
checking for X... libraries /usr/X11/lib, headers /usr/X11/include
...

The R-forge version also works.

>
> It seems a bit far fetched for the missing symbol to come from that library 
> though (but this is a
> JavaScripter/pythoneer talking :-).
>
> As I normally work on R-2.9, I just went back to R-2.8.1 and tried the 
> terminal procedure.
> Got the rgl examples running without problems. So that is not the cause of 
> the error message either.
>
> I also noticed you are using the latest rgl from R-Forge (83-751), while I 
> was using 83-3.
> Both versions work on my system.
>
> If someone could help out where _FT_Attach_File comes from ...
>
> Rob
>
>
> On Mar 3, 2009, at 2:48 PM, David Winsemius wrote:
>
>> Tried that method:
>> 
>> The compilation proceeded without error and was reported:
>> <snip quite a bit of material attached as rgl-compile.log>
>> ** building package indices ...
>> * DONE (rgl)
>> 
>> 
>> However, in R refreshing the Package Manager and attempting to load rgl 
>> fails to load with this error report:
>> 
>> Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> unable to load shared library 
>> '/Users/davidwinsemius/Library/R/2.8/library/rgl/libs/x86_64/rgl.so':
>> dlopen(/Users/davidwinsemius/Library/R/2.8/library/rgl/libs/x86_64/rgl.so, 
>> 6): Symbol not found: _FT_Attach_File
>> Referenced from: 
>> /Users/davidwinsemius/Library/R/2.8/library/rgl/libs/x86_64/rgl.so
>> Expected in: dynamic lookup
>> 
>> Error : .onLoad failed in 'loadNamespace' for 'rgl'
>> Error: package/namespace load failed for 'rgl'
>> <rgl-compile-log.txt>
>> 
>> -- thanks for all the eyeballs and ideas
>> 
>> David Winsemius
>> 
>> 
>> On Mar 3, 2009, at 5:16 PM, Rob Goedman wrote:
>> 
>>> David,
>>> 
>>> On my system libpng-config and xmkmf are in /usr/X11/bin, as on your 
>>> system.
>>> Adding /usr/X11/bin to my path did not help. I think /usr/X11R6 is just a 
>>> link back to /usr/X11.
>>> 
>>> Did you try the terminal suggestion?
>>> 
>>> Download rgl_0.83-3.tar.gz from CRAN, then in a terminal
>>> 
>>> Robs-Intel:~ rob$ pwd
>>> /Users/rob
>>> 
>>> Robs-Intel:~ rob$ cd Downloads/					# To 
>>> wherever the rgl.....tar.gz got stored
>>> 
>>> Robs-Intel:Downloads rob$ ls
>>> Cappuccino_Developer_Tools.pkg
>>> Changes.app
>>> Fluid_0.9.6.zip
>>> iphone_sdk_for_iphone_os_2.2.19m2621afinal.dmg
>>> rgl_0.83-3.tar.gz
>>> ...
>>> 
>>> Robs-Intel:Downloads rob$ R_ARCH=/x86_64 R CMD INSTALL 
>>> --configure-args='--disable-carbon' rgl_0.83-3.tar.gz
>>> * Installing to library 
>>> ‘/Library/Frameworks/R.framework/Resources/library’
>>> * Installing *source* package ‘rgl’ ...
>>> checking for gcc... gcc-4.2 -arch x86_64 -std=gnu99
>>> checking for C compiler default output file name... a.out
>>> checking whether the C compiler works... yes
>>> checking whether we are cross compiling... no
>>> ...
>>> 
>>> I know, it is not the ultimate solution, but it might help to know this 
>>> works on your system.
>>> 
>>> Rob
>
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-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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