Re: [R] R-2.3.0 make error

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Tue 02 May 2006 - 03:30:48 EST

"Wuming Gong" <wuming.gong@gmail.com> writes:

> Dear list,
>
> When compiling the R-2.3.0 on FC4 x86_64, I got the following errors:
>
> make[3]: Entering directory
> `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main'
> gcc -Wl,--export-dynamic -L/usr/local/lib64 -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 ../unix/libunix.a ../appl/libappl.a
> ../nmath/libnmath.a -lgfortran -lm -lgcc_s ../extra/zlib/libz.a
> ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a -lreadline -lncurses
> -ldl -lm
> ../appl/libappl.a(cmplxblas.o)(.text+0x1100a): In function `zrotg_':
> /project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5579:
> undefined reference to `z_abs'
> ../appl/libappl.a(cmplxblas.o)(.text+0x11069):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5585:
> undefined reference to `z_abs'
> ../appl/libappl.a(cmplxblas.o)(.text+0x11079):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5585:
> undefined reference to `z_abs'
> ../appl/libappl.a(cmplxblas.o)(.text+0x110de):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5586:
> undefined reference to `z_abs'
> ../appl/libappl.a(cmplxblas.o)(.text+0x11146):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5586:
> undefined reference to `z_abs'
> ../appl/libappl.a(cmplxblas.o)(.text+0x1116e):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5588:
> more undefined references to `z_abs' follow
> collect2: ld returned 1 exit status
> make[3]: *** [R.bin] Error 1
> make[3]: Leaving directory
> `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main'
> make[2]: *** [R] Error 2
> make[2]: Leaving directory
> `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main'
> make[1]: *** [R] Error 1
> make[1]: Leaving directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src'
> make: *** [R] Error 1
>
> Is there any way to fix this problem?

Hmm... It's not happening to me on a similar setup

$ uname -a
Linux janus 2.6.16-1.2096_FC4smp #1 SMP Wed Apr 19 16:01:54 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux

gcc -Wl,--export-dynamic -L/usr/local/lib64 -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 ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a -lblas -lgfortran -lm -lgcc_s ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a -lreadline -lncurses -ldl -lm

Apparently, you are configuring without a BLAS library, but it is not like I get into trouble by removing them from my setup. I'm puzzled.

You might check whether you need to upgrade something in your system.

-- 
   O__  ---- Peter Dalgaard             ุster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)                  FAX: (+45) 35327907

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Received on Tue May 02 03:33:55 2006

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