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Error compiling 64 bit R-devel on Leopard (package graphics)

14 messages · Raphael Gottardo at UBC, Duncan Murdoch, Federico Calboli +4 more

#
Hi All,

I am trying to compile R-devel on a new MacPro but I am having some difficulties compiling from source. 
The problem appears when I add the option --with-acqua, see the message error below. If I set --without-acqua, everything is fine.
I have searched the list for related issues but I could not find anything that would help me. There is an email from Vince Carey with a similar issue, but no fix is posted as far as I could tell.

Here is the end of the building process:

building package 'utils'
all.R is unchanged
make[4]: Nothing to be done for `iconvlist'.
building package 'grDevices'
all.R is unchanged
make[6]: `Makedeps' is up to date.
gcc -arch x86_64 -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -g -O2 -c chull.c -o chull.o
gcc -arch x86_64 -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -g -O2 -c devNull.c -o devNull.o
gcc -arch x86_64 -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -g -O2 -c devPicTeX.c -o devPicTeX.o
gcc -arch x86_64 -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -g -O2 -c devPS.c -o devPS.o
gcc -arch x86_64 -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -g -O2 -c devQuartz.c -o devQuartz.o
gcc -arch x86_64 -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -g -O2 -c init.c -o init.o
gcc -arch x86_64 -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -g -O2 -c qdBitmap.c -o qdBitmap.o
gcc -arch x86_64 -std=gnu99 -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include    -fPIC  -g -O2 -c qdPDF.c -o qdPDF.o
gcc -I../../../../include -I../../../include -I../../../../src/include -DHAVE_CONFIG_H -I/usr/local/include   -fPIC  -g -O2 -c qdCocoa.m -o qdCocoa.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o grDevices.so chull.o devNull.o devPicTeX.o devPS.o devQuartz.o init.o qdBitmap.o qdPDF.o qdCocoa.o -framework AppKit -L../../../../lib -lR -Wl,-framework -Wl,CoreFoundation
ld warning: in qdCocoa.o, file is not of required architecture
building package 'graphics'
all.R is unchanged
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library '/Users/gottarr/Downloads/trunk/library/grDevices/libs/grDevices.so':
  dlopen(/Users/gottarr/Downloads/trunk/library/grDevices/libs/grDevices.so, 6): Symbol not found: _QuartzCocoa_DeviceCreate
  Referenced from: /Users/gottarr/Downloads/trunk/library/grDevices/libs/grDevices.so
  Expected in: dynamic lookup
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
make[4]: *** [mklazy] Error 1
make[3]: *** [all] Error 2
make[2]: *** [R] Error 1
make[1]: *** [R] Error 1
make: *** [R] Error 1


Here is the options that I use during configure:
./configure CC='gcc -arch x86_64' CXX='g++ -arch x86_64' F77='gfortran -arch x86_64' FC='gfortran -arch x86_64' --with-blas='-framework vecLib' --with-lapack --with-aqua --with-readline --without-tcltk --with-system-zlib


I have successfully compiled R-devel on my older MacPro running the exact same version of Leopard with gcc/gfortran 4.2, just a few days ago. So I don't really understand what's going on. Am I missing something trivial?
Note that the new machine I have has a "Nehalem" processor, could this explains the difference?


Here are some more info in case you need it:
got10:trunk gottarr$ sw_versProductName:	Mac OS XProductVersion:	10.5.7
BuildVersion:	9J61
got10:trunk gottarr$ system_profiler | more
Hardware:

    Hardware Overview:

      Model Name: Mac Pro
      Model Identifier: MacPro4,1
      Processor Name: Quad-Core Intel Xeon
      Processor Speed: 2.93 GHz
      Number Of Processors: 2
      Total Number Of Cores: 8
      L2 Cache (per core): 256 KB
      L3 Cache (per processor): 8 MB
      Memory: 16 GB
      Processor Interconnect Speed: 6.4 GT/s
      Boot ROM Version: MP41.0081.B04
      SMC Version (system): 1.39f5
      SMC Version (processor tray): 1.39f5
      
Thanks in advance,

Raphael
#
On Jun 29, 2009, at 3:11 PM, Raphael Gottardo at UBC wrote:

            
You have forgotten to set OBJC accordingly and thus you get the wrong  
architecture for Obj-C files (see the error message). For an example  
on how to build multiple archs (64-bit is just another architecture)  
see R for Mac FAQ 2.5.

Cheers,
Simon
#
On 29/06/2009 10:30 PM, Christopher Desjardins wrote:
It's on CRAN now; perhaps the mirror you're using is a little slow to 
update?

Duncan Murdoch
#
On Jun 29, 2009, at 9:30 PM, Christopher Desjardins wrote:

            
The pre-built Mac binaries for R 2.9.1 are already up on the CRAN  
mirror network.

Is there a particular mirror where you are not seeing it?

Marc Schwartz
#
On Jun 29, 2009, at 22:39 , Duncan Murdoch wrote:

            
Probably quite a bit slow:

2009-06-26 13:29 R-2.9.1.dmg

so the Mac binary was actually out very early this time ... you could  
install it while having your afternoon tea on the R release date :).

Cheers,
Simon
#
In the bottomless pit of my stupidity I always wanted to ask the  
following, but I've always been too ashamed (or lazy) to ask. I always  
download the full dmg, but I never install any of the supplementary  
packages. Should I? only in case of a fresh installation (I'm  
upgrading now)? I have Xcode and X11 installed already anyway.

Federico
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
#
That was it. Thanks Simon!
I should have caught that.

Raphael
On Monday, June 29, 2009, at 06:10PM, "Simon Urbanek" <simon.urbanek at r-project.org> wrote:
#
That was it. Thanks Simon!
I should have caught that.

Raphael
On Monday, June 29, 2009, at 06:10PM, "Simon Urbanek" <simon.urbanek at r-project.org> wrote:
#
Hi,
On Jun 30, 2009, at 8:41 AM, Federico Calboli wrote:

            
I would use the full installer at least once :-)

It provides a tcl/tk library that R can use, as well as a gfortran  
compiler that can target the different Mac architectures (ppc/x86 32  
and 64 bit). While XCode will compile source package that only rely on  
C source, you'd be marooned w/o the gfortran compiler if a package has  
fortran source. That said, if you're just installing the binary  
package, then you probably wouldn't even notice.

I used the mini installer this time to upgrade from 2.9.0 to 2.9.1.

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

Contact Info: http://cbio.mskcc.org/~lianos/contact
#
On Jun 30, 2009, at 8:41 , Federico Calboli wrote:

            
This has nothing to do with Xcode or  X11. The full packages contains  
Tcl/Tk and GNU Fortran. You'll need Tcl/Tk is you want to use tcltk  
(the one that OS X ships with doesn't work) and you'll need GNU  
Fortran if you want to compile packages from sources that contain  
Fortran code. So if you a) don't use tcltk and b) don' t compile  
packages from sources you're fine wit the mini version.

Cheers,
Simon
#
On 30 Jun 2009, at 14:45, Simon Urbanek wrote:
I see... I always download the full dmg and 'double-click to install'.  
I was confused by the availability of the separate packages.

Cheers,

Fede


--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
#
Apparently I was incorrect ... http://cran.cnr.berkeley.edu/ is still 
showing 2.9.0 for Mac.
On 6/29/09 9:40 PM, Marc Schwartz wrote:

  
    
#
On Jun 30, 2009, at 13:28 , Christopher David Desjardins wrote:

            
Not for me (Universal R 2.9.1 for Mac OS X released on 2009/06/26) ...  
make sure you don't have some proxy in the way which is caching  
pages ...

Cheers,
S
#
Christopher,

Try to do a refresh/reload of the page, as I show on:

   http://cran.cnr.berkeley.edu/bin/macosx/

that the 2.9.1 dmg file is there.

It might be a page caching issue in your browser.

HTH,

Marc
On Jun 30, 2009, at 12:28 PM, Christopher David Desjardins wrote: