Re: [R] R-2.3.0 make error

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Tue 02 May 2006 - 16:51:21 EST

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

> Dear Peter,
>
> $ uname -a
> Linux bl3 2.6.15-1.1833_FC4smp #1 SMP Wed Mar 1 23:55:52 EST 2006
> x86_64 x86_64 x86_64 GNU/Linux
>
> When ./configure, I did not claim any options...
>
> Wuming

Hm. Which are your compilers? I have (in etc/Makeconf).

AR = ar
BLAS_LIBS =
C_VISIBILITY = -fvisibility=hidden
CC = gcc
CFLAGS = -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 -mtune=nocona
CPICFLAGS = -fpic
CPPFLAGS = -I/usr/local/include
CXX = g++
CXXCPP = g++ -E
CXXFLAGS = -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 -mtune=nocona
CXXPICFLAGS = -fpic

DYLIB_EXT = .so
DYLIB_LD = gcc
DYLIB_LDFLAGS = -shared
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO_C =

ECHO_N = -n
ECHO_T =
F77 = gfortran
F77_VISIBILITY = -fvisibility=hidden
FC = f95
FCFLAGS = -g -O2
FFLAGS = -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 -mtune=nocona
FLIBS = -lgfortran -lm -lgcc_s
FCPICFLAGS = -fpic
FPICFLAGS = -fpic
JAVA = /usr/bin/java
JAVA_HOME = /usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre
JAVA_LD_LIBRARY_PATH =
JAVA_LIBS = -L -ljvm

LAPACK_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRlapack
LIBM = -lm
LIBR =
LIBS =  -ldl -lm

LIBTOOL = $(SHELL) $(R_HOME)/bin/libtool LDFLAGS = -L/usr/local/lib64
R_ARCH =
RANLIB = ranlib
SAFE_FFLAGS = -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 -mtune=nocona -ffloat-store
SED = /bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++
SHLIB_CXXLDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FCLD = f95
SHLIB_FCLDFLAGS = -shared
SHLIB_FFLAGS =
SHLIB_LD = gcc
SHLIB_LDFLAGS = -shared
SHLIB_LIBADD =
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS)
TCLTK_CPPFLAGS = -I/usr/include -I/usr/include -I/usr/X11R6/include
TCLTK_LIBS = -L/usr/lib64 -ltcl8.4 -L/usr/lib64 -ltk8.4
-L/usr/X11R6/lib64 -lX11  

> On 01 May 2006 19:30:48 +0200, Peter Dalgaard <p.dalgaard@biostat.ku.dk> wrote:
> > "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
> >
>

-- 
   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 16:54:51 2006

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