Re: [R] solaris 64 build?

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Tue 10 Oct 2006 - 10:49:01 GMT

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 rkoenker@uiuc.edu Department of Economics
> vox: 217-333-4558 University of Illinois
> fax: 217-244-6678 Champaign, IL 61820
>
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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

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Received on Tue Oct 10 20:59:35 2006

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