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Problem compiling 64-bit R with X11 on Tiger
5 messages · Kasper Daniel Hansen, Christina Curtis, Simon Urbanek
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 at 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
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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 at 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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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 at 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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