R help - Jan 2007 - problem with compilation of R on Solaris 10 in x86

Dear List,
we're trying to install R on Solaris10 on a x86 (amd64).

During the installation we pass successfully the ./configure but we get 
an error through the built-in function "_isnan" which we see existing
in
/lib

When passing the command "make" we get :

gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2 
-I../../src/extra/pcre   -I. -I../../src/include -I../../src/include 
-I/usr/local/include -DHAVE_CONFIG_H -D__NO_MATH_INLINES  -g -O2 -c 
serialize.c -o serialize.o
In file included from ../../src/include/Rinternals.h:921,
                 from ../../src/include/Defn.h:72,
                 from serialize.c:29:
../../src/include/Rinlinedfuns.h: In function `fmin2_int':
../../src/include/Rinlinedfuns.h:602: warning: implicit declaration of 
function `__builtin_isnan'

[... and ...]
gcc -std=gnu99  -L/usr/local/lib -o R.bin Rmain.o CConverters.o 
CommandLineArgs.o  Rdynload.o Renviron.o RNG.o  apply.o arithmetic.o 
apse.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  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 graphics.o  identical.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 pcre.o platform.o  plot.o plot3d.o plotmath.o  
print.o printarray.o printvector.o printutils.o qsort.o  random.o 
regex.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  mkdtemp.o ../unix/libun!
ix.a ../appl/libappl.a ../nmath/libnmath.a -L../../lib -lRblas 
-L/opt/sfw/lib/gcc/i386-pc-solaris2.10/3.4.2 -L/usr/ccs/bin 
-L/opt/sfw/lib -lg2c -lm -lgcc_s  ../extra/zlib/libz.a  
../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a  
../extra/intl/libintl.a  -lreadline -lncurses -lnsl -lsocket -ldl -lm
Undefined                       first referenced
 symbol                             in file
__builtin_isnan                     arithmetic.o
ld: fatal: Symbol referencing errors. No output written to R.bin
collect2: ld returned 1 exit status


Thank's in advance for all hints how we could overcome this problem,
Wolfgang

 

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
. . . . .

Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et G?nomique Int?grative
IGBMC
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
http://www-bio3d-igbmc.u-strasbg.fr/~wraff
wolfgang.raffelsberger at igbmc.u-strasbg.fr

This has come up several times, all with long obselete versions of gcc. 
R does not use __builtin_isnan, but gcc does in its own (rather than 
Solaris') header files.  So it is an issue with the compiler, and note 
that 3.4.2 is an old (Sept 2004) version of the compiler.

If you are happy to use SunFreeware, they offer a pre-built R (apart for 
some unstated reason for the foreign package) at

http://www.sunfreeware.com/programlistintel10.html#R

and so it would appear that others have succeeded with more recent 
compilers.


On Wed, 31 Jan 2007, Wolfgang Raffelsberger wrote:
> Dear List,
> we're trying to install R on Solaris10 on a x86 (amd64).
>
> During the installation we pass successfully the ./configure but we get
> an error through the built-in function "_isnan" which we see
existing in
> /lib
>
> When passing the command "make" we get :
>
> gcc -std=gnu99 -I../../src/extra/zlib -I../../src/extra/bzip2
> -I../../src/extra/pcre   -I. -I../../src/include -I../../src/include
> -I/usr/local/include -DHAVE_CONFIG_H -D__NO_MATH_INLINES  -g -O2 -c
> serialize.c -o serialize.o
> In file included from ../../src/include/Rinternals.h:921,
>                 from ../../src/include/Defn.h:72,
>                 from serialize.c:29:
> ../../src/include/Rinlinedfuns.h: In function `fmin2_int':
> ../../src/include/Rinlinedfuns.h:602: warning: implicit declaration of
> function `__builtin_isnan'
>
> [... and ...]
> gcc -std=gnu99  -L/usr/local/lib -o R.bin Rmain.o CConverters.o
> CommandLineArgs.o  Rdynload.o Renviron.o RNG.o  apply.o arithmetic.o
> apse.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  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 graphics.o  identical.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 pcre.o platform.o  plot.o plot3d.o plotmath.o
> print.o printarray.o printvector.o printutils.o qsort.o  random.o
> regex.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  mkdtemp.o ../unix/libun!
> ix.a ../appl/libappl.a ../nmath/libnmath.a -L../../lib -lRblas
> -L/opt/sfw/lib/gcc/i386-pc-solaris2.10/3.4.2 -L/usr/ccs/bin
> -L/opt/sfw/lib -lg2c -lm -lgcc_s  ../extra/zlib/libz.a
> ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
> ../extra/intl/libintl.a  -lreadline -lncurses -lnsl -lsocket -ldl -lm
> Undefined                       first referenced
> symbol                             in file
> __builtin_isnan                     arithmetic.o
> ld: fatal: Symbol referencing errors. No output written to R.bin
> collect2: ld returned 1 exit status
>
>
> Thank's in advance for all hints how we could overcome this problem,
> Wolfgang
>
>
>
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> . . . . .
>
> Wolfgang Raffelsberger, PhD
> Laboratoire de BioInformatique et G?nomique Int?grative
> IGBMC
> 1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
> Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
> http://www-bio3d-igbmc.u-strasbg.fr/~wraff
> wolfgang.raffelsberger at igbmc.u-strasbg.fr
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 
Brian D. Ripley,                  ripley at 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