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compiling R 2.9.0 failed on Mac OS 10.5.6

2 messages · Martin Renner, Simon Urbanek

Original
Martin Renner
# 
I'm trying to compile R 2.9.0 from source on a MacBookPro (1.83 GHz  
Intel Core Duo, latest system software). I'm using the gfortran  
version from the R 2.9.0 GUI binary image and the following:

configure --disable-nls --with-aqua=no --enable-R-framework=no --with- 
x=no
make

This worked fine with R-2.8.1 but fails with the current version (see  
below). Using configure with defaults gives the same result. I have  
fink installed. Renaming /sw did not fix things either but resulted in  
a different failure (?). I don't know whether this is specific to my  
machine. I wondering whether there are any known conflicts with fink  
packages? Am I missing something obvious? Any pointers how to fix this  
would be much appreciated.

Martin


Martin Renner					
current address:
Alaska Maritime NWR
Homer, AK 99603, USA






R is now configured for i386-apple-darwin9.6.0

   Source directory:          /Users/martin/src/R-2.9.0
   Installation directory:    /usr/local

   C compiler:                gcc -std=gnu99  -g -O2
   Fortran 77 compiler:       gfortran  -g -O2

   C++ compiler:              g++  -g -O2
   Fortran 90/95 compiler:    gfortran -g -O2
   Obj-C compiler:	     gcc -g -O2

   Interfaces supported:      tcltk
   External libraries:        readline
   Additional capabilities:   PNG, JPEG, TIFF, iconv, cairo, ICU
   Options enabled:           shared BLAS, Java

   Recommended packages:      yes


[snip...]

gcc -std=gnu99 -I/Users/martin/src/R-2.9.0/src/extra/zlib -I/Users/ 
martin/src/R-2.9.0/src/extra/bzip2 -I/Users/martin/src/R-2.9.0/src/ 
extra/pcre  -I. -I../../src/include -I/Users/martin/src/R-2.9.0/src/ 
include -I/sw/include -I/usr/local/include -DHAVE_CONFIG_H    -g -O2 - 
c /Users/martin/src/R-2.9.0/src/main/attrib.c -o attrib.o
/Users/martin/src/R-2.9.0/src/main/attrib.c: In function ?do_class?:
/Users/martin/src/R-2.9.0/src/main/attrib.c:531: warning: implicit  
declaration of function ?S3Class?
/Users/martin/src/R-2.9.0/src/main/attrib.c:531: warning: assignment  
makes pointer from integer without a cast
/Users/martin/src/R-2.9.0/src/main/attrib.c: At top level:
/Users/martin/src/R-2.9.0/src/main/attrib.c:616: error: conflicting  
types for ?S3Class?
/Users/martin/src/R-2.9.0/src/main/attrib.c:531: error: previous  
implicit declaration of ?S3Class? was here
/Users/martin/src/R-2.9.0/src/main/attrib.c: In function  
?dimnamesgets1?:
/Users/martin/src/R-2.9.0/src/main/attrib.c:854: warning: implicit  
declaration of function ?asCharacterFactor?
/Users/martin/src/R-2.9.0/src/main/attrib.c:854: warning: return makes  
pointer from integer without a cast
make[3]: *** [attrib.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[2]: *** [R] Error 2
make[1]: *** [R] Error 1
make: *** [R] Error 1


and without fink:

making util.d from /Users/martin/src/R-2.9.0/src/main/util.c
/Users/martin/src/R-2.9.0/src/main/util.c:1572:28: error: unicode/ 
utypes.h: No such file or directory
/Users/martin/src/R-2.9.0/src/main/util.c:1573:26: error: unicode/ 
ucol.h: No such file or directory
/Users/martin/src/R-2.9.0/src/main/util.c:1574:26: error: unicode/ 
uloc.h: No such file or directory
/Users/martin/src/R-2.9.0/src/main/util.c:1575:27: error: unicode/ 
uiter.h: No such file or directory
make[3]: *** [util.d] Error 1
make[2]: *** [R] Error 2
make[1]: *** [R] Error 1
make: *** [R] Error 1
1 day later
Simon Urbanek
#
On Apr 24, 2009, at 3:36 PM, Martin Renner wrote:

            

      
      
      
    

        
The above works for me (modulo the modules issue*) on a clean system,  
so I suspect your setup. In fact given the mismatches in the sources  
below I'd suggest you check that you really have the correct 2.9.0  
sources and not some mix of old and new sources.  More see inline below.

Cheers,
Simon

            

      
      
      
    

        
I cannot reproduce this, either, but it is really strange since  
S3Class defined in the headers. Are you sure you have the correct  
sources?

            

      
      
      
    

        
--without-ICU may help here (the line numbers don't match with the R  
2.9.0 source, though...). For some reason it seems as if R can detect  
non-Apple ICU on your system but it doesn't quite work. Apple's ICU  
comes without headers, so we work around that, but only if there is no  
other ICU. Please send me the config.log so I can try to find out why.


* - this was discussed on R-devel, probably the easiest work-around is
echo R: > ~/Makefile