alloca() on FreeBSD (PR#7890)

Full_Name: Eric van Gyzen
Version: 2.1.0
OS: FreeBSD 5.4
Submission from: (NULL) (152.3.22.33)

R-2.1.0 fails to compile on the newest release of FreeBSD, complaining about
undefined references to __builtin_alloca.  On FreeBSD, alloca() is declared in
stdlib.h, not alloca.h as the R sources expect.  Therefore, HAVE_DECL_ALLOCA
does not get set, so the R sources declare alloca() after it has already been
#defined by stdlib.h.

A possible fix is to modify the configure script to look for the declaration of
alloca() in stdlib.h (perhaps after it fails to find it in alloca.h).
It is already supposed to, so it is not finding the declaration there 
either. If you look up the definition of

AC_CHECK_DECLS([alloca], , , [#include <alloca.h>])

it searches in stdlib.h.  Can you please send us the appropriate part of 
config.log?  It may be that this is failing because alloca.h is not found
(but AC_FUNC_ALLOCA is making the same assumptions).

Perhaps the easiest way out is to override the setting on FreeBSD: can 
you please confirm that manually changing

#define HAVE_DECL_ALLOCA 1

in config.h works?
This was previously reported in PR#7881.
So please don't open a new report on the subject!
Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595
One first reaction to your suggestions.
On Mon, 23 May 2005 vangyzen@stat.duke.edu wrote:
R-2.1.0 fails to compile on the newest release of FreeBSD, complaining about
undefined references to __builtin_alloca.  On FreeBSD, alloca() is declared in
stdlib.h, not alloca.h as the R sources expect.  Therefore, HAVE_DECL_ALLOCA
does not get set, so the R sources declare alloca() after it has already been
#defined by stdlib.h.

A possible fix is to modify the configure script to look for the declaration of
alloca() in stdlib.h (perhaps after it fails to find it in alloca.h).

It is already supposed to, so it is not finding the declaration there 
either. If you look up the definition of

AC_CHECK_DECLS([alloca], , , [#include <alloca.h>])

it searches in stdlib.h.  Can you please send us the appropriate part of 
config.log?  It may be that this is failing because alloca.h is not found
(but AC_FUNC_ALLOCA is making the same assumptions).

Perhaps the easiest way out is to override the setting on FreeBSD: can 
you please confirm that manually changing

#define HAVE_DECL_ALLOCA 1

in config.h works?
Changing "#define HAVE_DECL_ALLOCA" to 1
in line 81 of R-2.1.0/src/include/config.h
gives me the following stopping:

mkdir ../../../../library/grDevices/libs
building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/demo
mkdir ../../../library/graphics/po
mkdir ../../../library/graphics/man
Error in dyn.load(x, as.logical(local), as.logical(now)) :
         unable to load shared library 
'/usr/local/R-2.1.0/library/grDevices/libs/grDevices.so':
   /usr/local/R-2.1.0/library/grDevices/libs/grDevices.so: Undefined 
symbol "__builtin_alloca"
Execution halted
*** Error code 1
Stop in /usr/local/R-2.1.0/src/library/graphics.
*** Error code 1
Stop in /usr/local/R-2.1.0/src/library.
*** Error code 1
Stop in /usr/local/R-2.1.0/src.
*** Error code 1
Stop in /usr/local/R-2.1.0.

Because I have almost no skills in C, automake and autoconf I have no 
idea on how to go on, sorry.

Hopefully Eric makes considerable progress ...
Dr. Rainer Hurling                           Phone: (049) 551 69401-145
Abteilung Waldschutz, Sachgebiet Insekten    Fax:   (049) 551 69401-160
Nieders?chsische Forstliche Versuchsanstalt  Mobil: (049) 160 5835-143
Gr?tzelstra?e 2, D-37079 G?ttingen, GERMANY  Rainer.Hurling@nfv.gwdg.de

One first reaction to your suggestions.

ripley@stats.ox.ac.uk wrote:

On Mon, 23 May 2005 vangyzen@stat.duke.edu wrote:

R-2.1.0 fails to compile on the newest release of FreeBSD,  
complaining about
undefined references to __builtin_alloca.  On FreeBSD, alloca()  
is declared in
stdlib.h, not alloca.h as the R sources expect.  Therefore,  
HAVE_DECL_ALLOCA
does not get set, so the R sources declare alloca() after it has  
already been
#defined by stdlib.h.

A possible fix is to modify the configure script to look for the  
declaration of
alloca() in stdlib.h (perhaps after it fails to find it in  
alloca.h).

It is already supposed to, so it is not finding the declaration  
there either. If you look up the definition of
AC_CHECK_DECLS([alloca], , , [#include <alloca.h>])
it searches in stdlib.h.  Can you please send us the appropriate  
part of config.log?  It may be that this is failing because  
alloca.h is not found
(but AC_FUNC_ALLOCA is making the same assumptions).
Perhaps the easiest way out is to override the setting on FreeBSD:  
can you please confirm that manually changing
#define HAVE_DECL_ALLOCA 1
in config.h works?

Changing "#define HAVE_DECL_ALLOCA" to 1
in line 81 of R-2.1.0/src/include/config.h
gives me the following stopping:

mkdir ../../../../library/grDevices/libs
building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/demo
mkdir ../../../library/graphics/po
mkdir ../../../library/graphics/man
Error in dyn.load(x, as.logical(local), as.logical(now)) :
        unable to load shared library '/usr/local/R-2.1.0/library/ 
grDevices/libs/grDevices.so':
  /usr/local/R-2.1.0/library/grDevices/libs/grDevices.so: Undefined  
symbol "__builtin_alloca"
Execution halted
Did you run a new, clean build? From the output it seems as if you  
just changed the file in your old build and typed make - obviously  
that doesn't help at all, because the setting must the changed  
*before* you start building. So if you didn't do so, please remove  
the build, unpack the sources again, run configure, change the ALLOCA  
define and then build.

Cheers,
Simon
On Jun 7, 2005, at 12:36 PM, Rainer Hurling wrote:

One first reaction to your suggestions.

ripley@stats.ox.ac.uk wrote:

On Mon, 23 May 2005 vangyzen@stat.duke.edu wrote:

R-2.1.0 fails to compile on the newest release of FreeBSD,  
complaining about
undefined references to __builtin_alloca.  On FreeBSD, alloca()  is 
declared in
stdlib.h, not alloca.h as the R sources expect.  Therefore,  
HAVE_DECL_ALLOCA
does not get set, so the R sources declare alloca() after it has  
already been
#defined by stdlib.h.

A possible fix is to modify the configure script to look for the  
declaration of
alloca() in stdlib.h (perhaps after it fails to find it in  alloca.h).

It is already supposed to, so it is not finding the declaration  
there either. If you look up the definition of
AC_CHECK_DECLS([alloca], , , [#include <alloca.h>])
it searches in stdlib.h.  Can you please send us the appropriate  
part of config.log?  It may be that this is failing because  alloca.h 
is not found
(but AC_FUNC_ALLOCA is making the same assumptions).
Perhaps the easiest way out is to override the setting on FreeBSD:  
can you please confirm that manually changing
#define HAVE_DECL_ALLOCA 1
in config.h works?

Changing "#define HAVE_DECL_ALLOCA" to 1
in line 81 of R-2.1.0/src/include/config.h
gives me the following stopping:

mkdir ../../../../library/grDevices/libs
building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/demo
mkdir ../../../library/graphics/po
mkdir ../../../library/graphics/man
Error in dyn.load(x, as.logical(local), as.logical(now)) :
        unable to load shared library '/usr/local/R-2.1.0/library/ 
grDevices/libs/grDevices.so':
  /usr/local/R-2.1.0/library/grDevices/libs/grDevices.so: Undefined  
symbol "__builtin_alloca"
Execution halted

Did you run a new, clean build? From the output it seems as if you  just 
changed the file in your old build and typed make - obviously  that 
doesn't help at all, because the setting must the changed  *before* you 
start building. So if you didn't do so, please remove  the build, unpack 
the sources again, run configure, change the ALLOCA  define and then build.
Simon,
thank you, but I am absolute sure I made a new, clean built:

1.) untar R-2.1.0.tar.gz
2.) cd R-2.1.0
3.) ./configure
4.) edit src/include/config.h  [#define HAVE_DECL_ALLOCA 1]
5.) make

It seems to me that some files behave not like others in relation to 
alloca.h (resp. stdlib.h)?

Please tell me, if I can help in any way,
Rainer
This is a package, so it is not using config.h.  It is using

#ifdef HAVE_ALLOCA_H
#include <alloca.h>
#else
extern char *alloca(size_t);
#endif

and hence will have whatever the problem is with having that declaration.

The basic problem is that autoconf assumes that if alloca is defined 
anywhere, it is defined in alloca.h.  So we need to use something other 
than the standard macros.

Is there a macro FreeBSD defines?   If so it may be easiest to just make 
use of it.

On Jun 7, 2005, at 12:36 PM, Rainer Hurling wrote:

One first reaction to your suggestions.

ripley@stats.ox.ac.uk wrote:

On Mon, 23 May 2005 vangyzen@stat.duke.edu wrote:

R-2.1.0 fails to compile on the newest release of FreeBSD, complaining 
about
undefined references to __builtin_alloca.  On FreeBSD, alloca() is 
declared in
stdlib.h, not alloca.h as the R sources expect.  Therefore, 
HAVE_DECL_ALLOCA
does not get set, so the R sources declare alloca() after it has already 
been
#defined by stdlib.h.

A possible fix is to modify the configure script to look for the 
declaration of
alloca() in stdlib.h (perhaps after it fails to find it in alloca.h).

It is already supposed to, so it is not finding the declaration there 
either. If you look up the definition of
AC_CHECK_DECLS([alloca], , , [#include <alloca.h>])
it searches in stdlib.h.  Can you please send us the appropriate part of 
config.log?  It may be that this is failing because alloca.h is not found
(but AC_FUNC_ALLOCA is making the same assumptions).
Perhaps the easiest way out is to override the setting on FreeBSD: can you 
please confirm that manually changing
#define HAVE_DECL_ALLOCA 1
in config.h works?

Changing "#define HAVE_DECL_ALLOCA" to 1
in line 81 of R-2.1.0/src/include/config.h
gives me the following stopping:

mkdir ../../../../library/grDevices/libs
building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/demo
mkdir ../../../library/graphics/po
mkdir ../../../library/graphics/man
Error in dyn.load(x, as.logical(local), as.logical(now)) :
        unable to load shared library '/usr/local/R-2.1.0/library/ 
grDevices/libs/grDevices.so':
  /usr/local/R-2.1.0/library/grDevices/libs/grDevices.so: Undefined symbol 
"__builtin_alloca"
Execution halted
Did you run a new, clean build? From the output it seems as if you just 
changed the file in your old build and typed make - obviously that doesn't 
help at all, because the setting must the changed *before* you start 
building. So if you didn't do so, please remove the build, unpack the sources 
again, run configure, change the ALLOCA define and then build.

Cheers,
Simon

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Brian D. Ripley,                  ripley@stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595