[R-SIG-Mac] Problem compiling 64-bit R with X11 on Tiger

Fri Mar 14 16:17:35 CET 2008

On Mar 14, 2008, at 11:03 AM, Christina Curtis wrote:

> Thanks for the pointers. I actually had a 64bit X11 client installed  
> initially in /usr/local/lib64/X11/, but this wasn't found even  
> though the binaries were in the path.
> I only installed the older R-2.5 as a test since R-2.6.2 had given  
> errors concerning X11 while compiling. Simon, the X11R7 you  
> suggested fixed this problem and 2.6.2 works with X11.
> Now, I have another issue. Most packages seem to build fine from  
> source and can be loaded in a 64bit session. While the following  
> compiles without error, it gives an error upon loading:
>
> > library(EBImage)
> Error in dyn.load(x, as.logical(local), as.logical(now)) :
>         unable to load shared library '/Library/Frameworks/ 
> R.framework/Resources/library/EBImage/libs/x86_64/EBImage.so':
>   dlopen(/Library/Frameworks/R.framework/Resources/library/EBImage/ 
> libs/x86_64/EBImage.so, 6): Symbol not found: _gdk_display
>   Referenced from: /Library/Frameworks/R.framework/Resources/library/ 
> EBImage/libs/x86_64/EBImage.so
>   Expected in: dynamic lookup
>
> This package loads fine for 32-bit R on mac OSX and on linux 64-bit.  
> I can only guess that the error is due to the link between gtk/gdk  
> and X11 in the gtk+-2.10.0 library and the fact that I have both 64- 
> bit X11 (X11R7) and default X11R6 installed. I realize this is a  
> fairly specific problem, but any suggestions would be greatly  
> appreciated.
>

Did you install 64-bit GTK+ in the first place? A package won't give  
any errors at compile time if you don't have 64-bit binary of a  
certain library, because it is hoping to resolve dependencies at run  
time. I don't have 64-bit GTK+ (and I don't even know whether you can  
get one), so you're entirely on your own. Beware that GTK+ is an  
extreme pain to build - one of the many reasons is that they hard-code  
machine-specific information in the headers thus preventing a native  
"fat" build.

Cheers,
Simon

>
> On Fri, Mar 14, 2008 at 4:33 AM, Kasper Daniel Hansen <khansen at stat.berkeley.edu 
> > wrote:
> Why are you using R-2.5, when you try to compile R-2.6.2 from source?
> This seems to indicate that you do not really need an older version...
> Without being sure I would think that if you use 2.6.2 on Tiger you
> can use CarbonEL to get 64bit display quartz device functioning from
> the command line.
>
> Kasper
>
>
> On Mar 13, 2008, at 3:32 PM, Simon Urbanek wrote:
>
> > Christina,
> >
> > Tiger does not have 64-bit X11, so you either have to disable X11
> > support (--without-x) or install 64-bit version of X11 from  
> somewhere.
> > If you use the (rather old) R-25-br binary, then it expects X11 to  
> be
> > in /usr/local/X11R7 (you can download it at you own risk from
> > http://r.research.att.com/Xorg-quad.tar.gz
> > I didn't test it recently but it is the full client including  
> headers
> > etc. for all four architectures
> >
> > Cheers,
> > Simon
> >
> >
> > On Mar 13, 2008, at 5:49 PM, Christina Curtis wrote:
> >
> >> Hi All,
> >> I am having difficulty getting 64-bit R to compile properly on  
> Tiger
> >> 10.4.11
> >> .
> >> Specifically, I have tried both installing R2.6.2 from source and
> >> installing
> >> the R-25-br-quad.tar.gz binary, but both yield errors concerning  
> X11.
> >>
> >> When I build R-2.6.2.tar.gz from source, using the following
> >> commands:
> >>
> >> export PATH=/usr/local/lib64/X11/bin:$PATH
> >>
> >> ./configure CC='gcc-4.0 -arch x86_64' CXX='g++-4.0 -arch x86_64'
> >> \F77='
> >> gfortran-4.2 -arch x86_64' FC='gfortran-4.2 -arch x86_64'
> >> \r_arch=x86_64
> >> \--with-blas='-framework vecLib' --with-lapack --with-x \--with-
> >> system-zlib
> >> --build=x86_64-apple-darwin8.8.1 --prefix=/usr/local/lib64 --with-x
> >> --x-includes=/usr/local/lib64/X11/include/
> >> --x-libraries=/usr/local/lib64/X11/lib/ --with-readline \--without-
> >> iconv
> >> \CFLAGS="-g -O2 -march=nocona" CXXFLAGS="-g -O2 -march=nocona"
> >> \FFLAGS="-g
> >> -O2 -march=nocona" FCFLAGS="-g -O2 -march=nocona" \CPPFLAGS='-I/sw/
> >> include
> >> -I/sw/include/readline -I/usr/local/include -I/usr/local/include/
> >> readline
> >> -I/usr/include' \LDFLAGS='-L/usr/local/lib/x86_64 -L/usr/local/lib
> >> -L/usr/lib -L/sw/lib'
> >>
> >> compilation appears fine apart from the following error:
> >> configure: error: --with-x=yes (default) and X11 headers/libs are  
> not
> >> available
> >>
> >> I am not certain as to why this occurs given that the binaries are
> >> in the
> >> PATH.
> >>
> >> I have also followed the guide outlined on the experimental build
> >> page:
> >> http://r.research.att.com/exp/
> >> and in a previous post:
> >> http://www.mail-archive.com/r-sig-mac@stat.math.ethz.ch/msg01673.html
> >> for installing the R-2.5 quad binary. R-25-br-quad.tar.gz installs
> >> fine, but
> >> despite having the X11 64 bit client installed in /usr/local/lib64/
> >> X11* *,
> >> gives an error
> >>
> >>> x11()
> >> Error in x11() : X11 module cannot be loaded
> >> In addition: Warning message:
> >> unable to load shared library
> >> '/Library/Frameworks/R.framework/Resources/modules/x86_64/ 
> R_X11.so':
> >> dlopen(/Library/Frameworks/R.framework/Resources/modules/x86_64/
> >> R_X11.so,
> >> 6): Library not loaded: /usr/local/X11R7/lib/libSM.6.dylib
> >> Referenced from:
> >> /Library/Frameworks/R.framework/Resources/modules/x86_64/R_X11.so
> >> Reason: image not found
> >>
> >>> sessionInfo()
> >> R version 2.5.0 Patched (2007-05-02 r41420)
> >> x86_64-apple-darwin8.9.1
> >> locale:
> >> C
> >> attached base packages:
> >> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"
> >> "methods"
> >> [7] "base"
> >>
> >> I have tried creating a soft link from /usr/local/lib64/X11 to
> >> /usr/local/X11R7, but this results in the error:
> >>
> >> Error in x11() : X11 module cannot be loaded
> >> In addition: Warning message:
> >> unable to load shared library
> >> '/Library/Frameworks/R.framework/Resources/modules/x86_64/ 
> R_X11.so':
> >> dlopen(/Library/Frameworks/R.framework/Resources/modules/x86_64/
> >> R_X11.so,
> >> 6): Library not loaded: /usr/local/X11R7/lib/libSM.6.dylib
> >> Referenced from:
> >> /Library/Frameworks/R.framework/Resources/modules/x86_64/R_X11.so
> >> Reason: no suitable image found.  Did find:
> >>       /usr/local/X11R7/lib/libSM.6.dylib: mach-o, but wrong
> >> architecture
> >>
> >> Is there a binary available for X11R7?
> >> Any other solutions as to how to get 64-bit R functioning properly
> >> with X11
> >> on Tiger.
> >>
> >> Thanks in advance,
> >> C
> >>
> >>      [[alternative HTML version deleted]]
> >>
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> >>
> >>
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