[R] solaris 64 build?

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[R] solaris 64 build?

RKoenker
We have a solaris/sparc machine that has been running an old version
of R-devel:  Version 2.2.0 Under development (unstable) (2005-06-04  
r34577)
which was built as m64 from sources.  Attempting to upgrade to 2.4.0  
the configure step
goes ok, but I'm getting early on from make:

> gcc -m64  -L/opt/sfw/lib/sparcv9  -L/usr/lib/sparcv9
> -L/usr/openwin/lib/sparcv9  -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/libunix.a
> ../appl/libappl.a ../nmath/libnmath.a -L../../lib -lRblas
> -L/usr/local/encap/gf7764-3.4.3+2/lib/gcc/sparc64-sun-solaris2.9/3.4.3
> -L/usr/ccs/bin/sparcv9 -L/usr/ccs/bin -L/usr/ccs/lib
> -L/usr/local/encap/gf7764-3.4.3+2/lib/sparcv9
> -L/usr/local/encap/gf7764-3.4.3+2/lib -lg2c -lm -lgcc_s
> ../extra/zlib/libz.a  ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
> ../extra/intl/libintl.a  -lreadline -ltermcap -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

I've tried to look at the difference in outcomes in the old R-devel
version --  if I touch arithmetic.c  there and then type make I get a  
something
almost the same as above except for the following  bits that are new  
to 2.4.0
(this diff is after replacing spaces with linebreaks obviously.)

ysidro.econ.uiuc.edu% diff t0 t1
54a55
 > localecharset.o
81a83
 > rlocale.o
101a104
 > mkdtemp.o
104a108,109
 > -L../../lib
 > -lRblas


Has there been some change in the way that Rblas is used, or in
isnan?  It didn't seem so from a look at arithmetic.c, but this is well
beyond me.

I hope that someone sees something suspicious, or could point me
toward a better diagnostic.  Thanks,

Roger


url:    www.econ.uiuc.edu/~roger            Roger Koenker
email    [hidden email]            Department of Economics
vox:     217-333-4558                University of Illinois
fax:       217-244-6678                Champaign, IL 61820

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Re: [R] solaris 64 build?

Brian Ripley
Which Solaris is this?  I am not seeing any problems with our Solaris 8
systems.  Was the compiler built on that exact system?  What gcc options
were used (-std=gnu99, as recommended, for instance)?

It looks like a system header problem: __builtin_isnan ought to be
built in, not an external entry point.  Since R does not use it, you need
to trace through the headers to see why isnan is expanding to it.

On Thu, 5 Oct 2006, roger koenker wrote:

> We have a solaris/sparc machine that has been running an old version
> of R-devel:  Version 2.2.0 Under development (unstable) (2005-06-04
> r34577)
> which was built as m64 from sources.  Attempting to upgrade to 2.4.0
> the configure step
> goes ok, but I'm getting early on from make:
>
>> gcc -m64  -L/opt/sfw/lib/sparcv9  -L/usr/lib/sparcv9
>> -L/usr/openwin/lib/sparcv9  -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/libunix.a
>> ../appl/libappl.a ../nmath/libnmath.a -L../../lib -lRblas
>> -L/usr/local/encap/gf7764-3.4.3+2/lib/gcc/sparc64-sun-solaris2.9/3.4.3
>> -L/usr/ccs/bin/sparcv9 -L/usr/ccs/bin -L/usr/ccs/lib
>> -L/usr/local/encap/gf7764-3.4.3+2/lib/sparcv9
>> -L/usr/local/encap/gf7764-3.4.3+2/lib -lg2c -lm -lgcc_s
>> ../extra/zlib/libz.a  ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a
>> ../extra/intl/libintl.a  -lreadline -ltermcap -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
>
> I've tried to look at the difference in outcomes in the old R-devel
> version --  if I touch arithmetic.c  there and then type make I get a
> something
> almost the same as above except for the following  bits that are new
> to 2.4.0
> (this diff is after replacing spaces with linebreaks obviously.)
>
> ysidro.econ.uiuc.edu% diff t0 t1
> 54a55
> > localecharset.o
> 81a83
> > rlocale.o
> 101a104
> > mkdtemp.o
> 104a108,109
> > -L../../lib
> > -lRblas
>
>
> Has there been some change in the way that Rblas is used, or in
> isnan?  It didn't seem so from a look at arithmetic.c, but this is well
> beyond me.
>
> I hope that someone sees something suspicious, or could point me
> toward a better diagnostic.  Thanks,
>
> Roger
>
>
> url:    www.econ.uiuc.edu/~roger            Roger Koenker
> email    [hidden email]            Department of Economics
> vox:     217-333-4558                University of Illinois
> fax:       217-244-6678                Champaign, IL 61820
>
> ______________________________________________
> [hidden email] 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,                  [hidden email]
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

______________________________________________
[hidden email] 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.