X11 missing? ... was Re: [R] rgl persp3d bounding box color problem.
David, I've created, as suggested by Casper and Brian, a .Rprofile in my home directory with a single line: Sys.setenv(PATH="/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/ X11/bin") I think there needs to be a return after the line (could that have caused my problem earlier???). This indeed fixes the install from within R.app!!!!! Could it be that your system picks up another libfreetype.a. Does Spotlight show other libfreetype's? Or good ol' find in the terminal: Robs-Intel:~ rob$ sudo find /usr -name "libfreetype.*" -print Password: /usr/local/gtk2/lib/libfreetype.6.3.8.dylib /usr/local/gtk2/lib/libfreetype.6.dylib /usr/local/gtk2/lib/libfreetype.dylib /usr/local/gtk2/lib/libfreetype.la /usr/local/lib/libfreetype.a /usr/local/lib/libfreetype.la /usr/X11/lib/libfreetype.6.3.16.dylib /usr/X11/lib/libfreetype.6.dylib /usr/X11/lib/libfreetype.dylib /usr/X11/lib/libfreetype.la /usr/X11R6 1/lib/libfreetype.a Robs-Intel:~ rob$ Just to make sure, I just reinstalled Simon's devpack4 and installed both versions of rgl (83-3 and 83-751). Both build, install and run fine from within R.app. Rob
On Mar 4, 2009, at 8:34 AM, David Winsemius wrote:
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