Skip to content

R-beta_2010-10-02_r53128 fails to compile on FreeBSD

8 messages · Peter Dalgaard, Brian Ripley, Rainer Hurling

Original
Rainer Hurling
# 
I tried to compile R-beta_2010-10-02_r53128 on FreeBSD 9.0-CURRENT 
(amd64) with gcc-4.4.5 and it fails:

-----------------------------------------
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 
-I../../src/extra/pcre  -I../../src/extra   -I. -I../../src/include 
-I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -g -O2 -c 
sysutils.c -o sysutils.o
sysutils.c: In function 'R_system':
sysutils.c:289: warning: implicit declaration of function 'WIFEXITED'
sysutils.c:289: warning: implicit declaration of function 'WEXITSTATUS'
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 
-I../../src/extra/pcre  -I../../src/extra   -I. -I../../src/include 
-I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -g -O2 -c 
unique.c -o unique.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 
-I../../src/extra/pcre  -I../../src/extra   -I. -I../../src/include 
-I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -g -O2 -c 
util.c -o util.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 
-I../../src/extra/pcre  -I../../src/extra   -I. -I../../src/include 
-I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -g -O2 -c 
version.c -o version.o
gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 
-I../../src/extra/pcre  -I../../src/extra   -I. -I../../src/include 
-I../../src/include -I/usr/local/include -DHAVE_CONFIG_H   -g -O2 -c 
vfonts.c -o vfonts.o
gfortran   -g -O2 -c xxxpr.f -o xxxpr.o
ar cr libR.a CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o 
agrep.o apply.o arithmetic.o array.o attrib.o base.o bind.o builtin.o 
character.o coerce.o colors.o complex.o connections.o context.o cov.o 
cum.o dcf.o datetime.o debug.o deparse.o deriv.o devices.o dotcode.o 
dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o 
format.o fourier.o gevents.o gram.o gram-ex.o gramLatex.o gramRd.o 
graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o 
lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o 
model.o names.o objects.o optim.o optimize.o options.o par.o paste.o 
platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o 
printutils.o qsort.o random.o raw.o registration.o relop.o rlocale.o 
saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o 
sprintf.o startup.o subassign.o subscript.o subset.o summary.o 
sysutils.o unique.o util.o version.o vfonts.o xxxpr.o libs/*o
ranlib libR.a
gcc -std=gnu99 -export-dynamic -L/usr/local/lib -o R.bin Rmain.o libR.a 
-L../../lib -lRblas 
-L/usr/local/lib/gcc44/gcc/x86_64-portbld-freebsd9.0/4.4.5 
-L/usr/local/x86_64-portbld-freebsd9.0/lib -L/usr/local/lib/gcc44 
-lgfortran -lm  /usr/local/lib/libintl.so /usr/local/lib/libiconv.so 
-Wl,-rpath -Wl,/usr/local/lib -lreadline -llzma -lm -liconv -licuuc 
-licui18n
libR.a(sysutils.o)(.text+0x1d5d): In function `R_system':
/usr/local/R-beta/src/main/sysutils.c:289: undefined reference to 
`WIFEXITED'
libR.a(sysutils.o)(.text+0x1d76):/usr/local/R-beta/src/main/sysutils.c:289: 
undefined reference to `WEXITSTATUS'
libR.a(sys-unix.o)(.text+0x475): In function `do_system':
/usr/local/R-beta/src/unix/sys-unix.c:290: undefined reference to 
`WIFEXITED'
libR.a(sys-unix.o)(.text+0x551):/usr/local/R-beta/src/unix/sys-unix.c:290: 
undefined reference to `WEXITSTATUS'
*** Error code 1
Stop in /usr/local/R-beta/src/main.
*** Error code 1
Stop in /usr/local/R-beta/src/main.
*** Error code 1
Stop in /usr/local/R-beta/src.
*** Error code 1
Stop in /usr/local/R-beta.
-----------------------------------------

Is this a known error? I would really appreciate if someone could give 
me a hint.

Please let me know if more information is needed.

Thanks in advance,
Rainer Hurling
Peter Dalgaard
#
On 10/03/2010 04:24 PM, Rainer Hurling wrote:
Thanks for the report. WIFEXITED/WEXITSTATUS are usually defined in
<sys/wait.h> (usually /usr/include/sys/wait.h). Do you have any
indication that this might be skipped? (configure output, etc.)

I'm not quite sure by which mechanism gcc is expected to include
sys/wait.h, but the offending code is inside

#ifdef HAVE_SYS_WAIT_H

which configure is supposed to set only if it is available and POSIX
compatible.

Any chance you switched platform features (e.g. upgraded gcc) without
reconfiguring?

-pd

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
      #
    

  


  

      
On Sun, 3 Oct 2010, Rainer Hurling wrote:

        

            

      
      
      
    

        
Not known, and as it is a POSIX construction almost all OSes have it.
Can you try (in sysutils.c and sys-unix.c) replacing

#ifdef HAVE_SYS_WAIT_H

by

#if defined(HAVE_SYS_WAIT_H) && defined(WEXITSTATUS)

?

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Rainer Hurling
    

    

      
      #
    

  


  

      
On 03.10.2010 17:10 (UTC+1), Prof Brian Ripley wrote:

            

      
      
      
    

        
Hmmm. It seems its implementation in FreeBSD (CURRENT) is a little 
different from other OSes?

            

      
      
      
    

        
Yes, with this patch in both files all works again. I tried it with 
gcc-4.4.5 and gcc-4.5.2. Is there any chance to get it in the release 
(R-2.12.0)?

As always you hit the goal. Thank you very much for the quick help,
Rainer Hurling

  
  


  


      

    

    

      
      

        


  

        

      Rainer Hurling
    

    

      
      #
    

  


  

      
On 03.10.2010 17:08 (UTC+1), Peter Dalgaard wrote:

            

      
      
      
    

        
I think you are right, see the posting of Brian Ripley. With his 
suggested patch it works again.

            

      
      
      
    

        
No, nothing I am aware of. But 9.0-CURRENT is the development platform 
of FreeBSD and my system is very recent ;-)

            

      
      
      
    

        
Many thanks for your answer,
Rainer Hurling

            

      
      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Brian Ripley
    

    

      
      #
    

  


  

      
On Sun, 3 Oct 2010, Rainer Hurling wrote:

        
...

            

      
      
      
    

        
Yes, of course.  (After a little more testing on other platforms.)

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Peter Dalgaard
    

    

      
      #
    

  


  

      
On 10/03/2010 05:58 PM, Prof Brian Ripley wrote:

            

      
      
      
    

        
Only it strikes me that it might be plugging the wrong hole. I.e., that
the real issue is that somehow we're not including sys/wait.h in all
cases. Would it perchance also work to have

#ifdef HAVE_SYS_WAIT_H
#include <sys/wait.h>
#endif

somewhere at the top of the files that use the two macros (sysutils.c
and sys-unix.c AFAICS).

"&& defined(WEXITSTATUS)" probably won't break anything that wasn't
already broken, but it does insert a default definition that could
conflict with the one intended for the OS (that's what include files and
macros are for, after all).

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Rainer Hurling
    

    

      
      #
    

  


  

      
On 03.10.2010 18:38 (UTC+1), Peter Dalgaard wrote:

            

      
      
      
    

        
Just as a note. This (#include<sys/wait.h>) also works on FreeBSD.

Rainer Hurling