[R-SIG-Mac] X11 missing? ... was Re: [R] rgl persp3d bounding box color problem.
David Winsemius
dwinsemius at comcast.net
Wed Mar 4 17:34:00 CET 2009
I appreciate all the help. For me:
> Sys.getenv("PATH")
PATH
"/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"
I suspect that I have in the past read that the system $PATH is not
the correct place to let R know where libraries are located but I
certainly had forgotten that important fact. I will re-read the
Installation Manual and modify my .Rprofile accordingly.
I have loaded the devpack4 from Urbanek's website in the past and I do
have what appears to be a similar version of 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
Thank you all once more;
David Winsemius
On Mar 4, 2009, at 2:53 AM, Prof Brian Ripley wrote:
> 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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