[R-SIG-Mac]Problem building 1.5.0 from sources
Don MacQueen
dmacq@ucscalumni.com
Thu, 16 May 2002 06:52:00 -0700
I have Jan de Leeuw's build of Darwin R 1.5.0 installed and running
happily; thank you very much.
I would also like to be able to build from sources. I do this on a
Solaris machine at work, but haven't been able to do it on either of
two OS X machines.
I've included a ton of output below, but here's one error message
from the make step that may be a major clue:
symbol _tgoto used from dynamic library
/usr/lib/libm.dylib(tgoto.o) not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_tgoto.o)
which suggests a version mismatch. /usr/lib/libm.dylib is from the
Developer Tools.
There are also many error messages of this form:
/usr/bin/ld: warning unused multiple definitions of symbol _matherr
arithmetic.o definition of _matherr in section (__TEXT,__text)
/usr/lib/libm.dylib(s_matherr.o) unused definition of _matherr
/usr/bin/ld: warning unused multiple definitions of symbol _regerror
regex.o definition of _regerror in section (__TEXT,__text)
/usr/lib/libm.dylib(regerror.o) unused definition of _regerror
What am I doing wrong? Or what's wrong with what's installed in my system?
Thanks for any suggestions.
-Don
I am inclined to infer that since I previously installed R 1.4.1 from
fink I already have all extra libraries and whatnot that R needs,
installed from fink. And everything in fink that I believe R uses is
up to date.
David Richmond forwarded a tip from Luke and Stefano that I'm sure
cleared up some problems. But not all.
configure command (I actually tried it first with the LDFLAGS and
CPPFLAGS supplied in config.site, makes no difference):
../source/configure --prefix=/Users/macq/R/R-1.5.0
CPPFLAGS="-I/sw/include" LDFLAGS="-L/sw/lib"
--with-tcl-config=/sw/lib/tclConfig.sh
--with-tk-config=/sw/lib/tkConfig.sh > & dhm.config.log
Output from configure doesn't have any messages that I can recognize
as indicating trouble.
(I compared my Makeconf file with David's and there are only trivial
differences; thank you David)
What version of the Developer Tools should I have??? I have the
December 2001, which as far as I know is the latest non-beta version.
Should I have used fink to remove 1.4.1 first?
The output from make starts with this:
make[1]: Nothing to be done for `R'.
make[1]: Nothing to be done for `R'.
make[2]: Nothing to be done for `R'.
make[1]: Nothing to be done for `R'.
mkdir -p -- ../share/R
mkdir -p -- ../share/make
[already, this is puzzling; "Nothing to be done" makes no sense when
nothing has been done yet except configure]
Output from make looks good for quite a while. Then:
cc -no-cpp-precomp -I. -I../../src/include
-I../../../source/src/include -I/sw/include -DHAVE_CONFIG_H -g -O2
-c ../../../source/src/main/names.c -o names.o
In file included from ../../../source/src/main/names.c:27:
../../../source/src/include/Defn.h:385: warning: variable `R_FunTab'
is implicitly extern
and still later
cc -no-cpp-precomp -I. -I../../src/include
-I../../../source/src/include -I/sw/include -DHAVE_CONFIG_H -g -O2
-c ../../../source/src/main/names.c -o names.o
In file included from ../../../source/src/main/names.c:27:
../../../source/src/include/Defn.h:385: warning: variable `R_FunTab'
is implicitly extern
Then towards the end a whole slew of bad looking messages:
cc -L/sw/lib -o R.bin CConverters.o Rdynload.o RNG.o apply.o
arithmetic.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 devPS.o devPicTeX.o deparse.o deriv.o devices.o
dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o
eval.o format.o fourier.o gram.o gram-ex.o graphics.o identical.o
internet.o iosupport.o lapack.o list.o logic.o main.o match.o
memory.o model.o names.o objects.o optim.o optimize.o options.o par.o
paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o
printvector.o printutils.o qsort.o random.o regex.o relop.o
saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o
sprintf.o subassign.o subscript.o subset.o summary.o unique.o util.o
version.o vfonts.o xxxpr.o ../unix/libunix.a ../appl/libappl.a
../nmath/libnmath.a -lf77blas -latlas -L/sw/lib -lreadline -ldl
-lncurses -lm -lg2c -lcc_dynamic -lSystem -lbz2 -lz -lreadline -ldl
-lncurses -lm
/usr/bin/ld: warning multiple definitions of symbol _regcomp
regex.o definition of _regcomp in section (__TEXT,__text)
/usr/lib/libm.dylib(regcomp.o) definition of _regcomp
/usr/bin/ld: warning multiple definitions of symbol _regexec
regex.o definition of _regexec in section (__TEXT,__text)
/usr/lib/libm.dylib(regexec.o) definition of _regexec
/usr/bin/ld: warning multiple definitions of symbol _regfree
regex.o definition of _regfree in section (__TEXT,__text)
/usr/lib/libm.dylib(regfree.o) definition of _regfree
/usr/bin/ld: warning multiple definitions of symbol _UP
/sw/lib/libreadline.dylib(terminal.so) definition of _UP
/usr/lib/libm.dylib(curses.o) definition of _UP
/usr/bin/ld: warning multiple definitions of symbol _PC
/sw/lib/libreadline.dylib(terminal.so) definition of _PC
/usr/lib/libm.dylib(curses.o) definition of _PC
/usr/bin/ld: warning multiple definitions of symbol _BC
/sw/lib/libreadline.dylib(terminal.so) definition of _BC
/usr/lib/libm.dylib(curses.o) definition of _BC
/usr/bin/ld: warning suggest use of -bind_at_load, as lazy binding
may result in errors or different symbols being used
symbol _tgoto used from dynamic library /usr/lib/libm.dylib(tgoto.o)
not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_tgoto.o)
symbol _tputs used from dynamic library /usr/lib/libm.dylib(tputs.o)
not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_tputs.o)
symbol _ospeed used from dynamic library /usr/lib/libm.dylib(tputs.o)
not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_tputs.o)
symbol _tgetflag used from dynamic library
/usr/lib/libm.dylib(termcap.o) not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_termcap.o)
symbol _tgetent used from dynamic library
/usr/lib/libm.dylib(termcap.o) not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_termcap.o)
symbol _tgetnum used from dynamic library
/usr/lib/libm.dylib(termcap.o) not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_termcap.o)
symbol _tgetstr used from dynamic library
/usr/lib/libm.dylib(termcap.o) not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_termcap.o)
symbol _curscr used from dynamic library
/usr/lib/libm.dylib(curses.o) not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_data.o)
symbol _stdscr used from dynamic library
/usr/lib/libm.dylib(curses.o) not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_data.o)
symbol _COLS used from dynamic library /usr/lib/libm.dylib(curses.o)
not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_setup.o)
symbol _LINES used from dynamic library /usr/lib/libm.dylib(curses.o)
not from earlier dynamic library
/sw/lib/libncurses.dylib.5(lib_setup.o)
/usr/bin/ld: warning unused multiple definitions of symbol _matherr
arithmetic.o definition of _matherr in section (__TEXT,__text)
/usr/lib/libm.dylib(s_matherr.o) unused definition of _matherr
/usr/bin/ld: warning unused multiple definitions of symbol _regerror
regex.o definition of _regerror in section (__TEXT,__text)
/usr/lib/libm.dylib(regerror.o) unused definition of _regerror
/usr/bin/ld: warning unused multiple definitions of symbol _signgam
"link editor" definition of _signgam in section (__DATA,__common)
/usr/lib/libm.dylib(s_signgam.o) unused definition of _signgam
/usr/bin/ld: warning unused multiple definitions of symbol _BC
/sw/lib/libreadline.dylib(terminal.so) definition of _BC
/sw/lib/libncurses.dylib(lib_termcap.o) unused definition of _BC
/usr/bin/ld: warning unused multiple definitions of symbol _PC
/sw/lib/libreadline.dylib(terminal.so) definition of _PC
/sw/lib/libncurses.dylib(lib_tputs.o) unused definition of _PC
/usr/bin/ld: warning unused multiple definitions of symbol _UP
/sw/lib/libreadline.dylib(terminal.so) definition of _UP
/sw/lib/libncurses.dylib(lib_termcap.o) unused definition of _UP
/usr/bin/ld: warning unused multiple definitions of symbol _tgoto
/usr/lib/libm.dylib(tgoto.o) definition of _tgoto
/sw/lib/libncurses.dylib(lib_tgoto.o) unused definition of _tgoto
/usr/bin/ld: warning unused multiple definitions of symbol _tputs
/usr/lib/libm.dylib(tputs.o) definition of _tputs
/sw/lib/libncurses.dylib(lib_tputs.o) unused definition of _tputs
/usr/bin/ld: warning unused multiple definitions of symbol _ospeed
/usr/lib/libm.dylib(tputs.o) definition of _ospeed
/sw/lib/libncurses.dylib(lib_tputs.o) unused definition of _ospeed
/usr/bin/ld: warning unused multiple definitions of symbol _tgetflag
/usr/lib/libm.dylib(termcap.o) definition of _tgetflag
/sw/lib/libncurses.dylib(lib_termcap.o) unused definition of _tgetflag
/usr/bin/ld: warning unused multiple definitions of symbol _tgetent
/usr/lib/libm.dylib(termcap.o) definition of _tgetent
/sw/lib/libncurses.dylib(lib_termcap.o) unused definition of _tgetent
/usr/bin/ld: warning unused multiple definitions of symbol _tgetnum
/usr/lib/libm.dylib(termcap.o) definition of _tgetnum
/sw/lib/libncurses.dylib(lib_termcap.o) unused definition of _tgetnum
/usr/bin/ld: warning unused multiple definitions of symbol _tgetstr
/usr/lib/libm.dylib(termcap.o) definition of _tgetstr
/sw/lib/libncurses.dylib(lib_termcap.o) unused definition of _tgetstr
/usr/bin/ld: warning unused multiple definitions of symbol _curscr
/usr/lib/libm.dylib(curses.o) definition of _curscr
/sw/lib/libncurses.dylib(lib_data.o) unused definition of _curscr
/usr/bin/ld: warning unused multiple definitions of symbol _stdscr
/usr/lib/libm.dylib(curses.o) definition of _stdscr
/sw/lib/libncurses.dylib(lib_data.o) unused definition of _stdscr
/usr/bin/ld: warning unused multiple definitions of symbol _COLS
/usr/lib/libm.dylib(curses.o) definition of _COLS
/sw/lib/libncurses.dylib(lib_setup.o) unused definition of _COLS
/usr/bin/ld: warning unused multiple definitions of symbol _LINES
/usr/lib/libm.dylib(curses.o) definition of _LINES
/sw/lib/libncurses.dylib(lib_setup.o) unused definition of _LINES
and a bit later
cc -bundle -bundle_loader ../../../bin/R.bin -L/sw/lib -o R_X11.so
dataentry.lo devX11.lo rotated.lo rbitmap.lo -lSM -lICE
-L/usr/X11R6/lib -lX11 -ljpeg -lpng -lz -lbz2 -lz -lreadline -ldl
-lncurses -lm
/usr/bin/ld: warning multiple definitions of symbol _regcomp
../../../bin/R.bin definition of _regcomp
/usr/lib/libm.dylib(regcomp.o) definition of _regcomp
And finally at the end:
cc -no-cpp-precomp -I../../../../include -I/sw/include
-I/usr/X11R6/include -I/sw/include -fno-common -g -O2 -c
../../../../../source/src/library/tcltk/src/tcltk.c -o tcltk.o
cc -bundle -bundle_loader ../../../../bin/R.bin -o tcltk.so tcltk.o
-L/sw/lib -lm
/usr/bin/ld: Undefined symbols:
_TclFreeObj
_Tcl_CreateCommand
_Tcl_CreateInterp
_Tcl_DoOneEvent
_Tcl_Eval
_Tcl_GetDoubleFromObj
_Tcl_GetIntFromObj
_Tcl_GetObjResult
_Tcl_GetString
_Tcl_GetVar2Ex
_Tcl_Init
_Tcl_ListObjAppendElement
_Tcl_ListObjGetElements
_Tcl_NewDoubleObj
_Tcl_NewIntObj
_Tcl_NewObj
_Tcl_SetResult
_Tcl_SetStringObj
_Tcl_SetVar2Ex
_Tcl_StaticPackage
_Tk_Init
_Tk_SafeInit
/usr/bin/ld: warning unused multiple definitions of symbol _matherr
../../../../bin/R.bin definition of _matherr
/usr/lib/libm.dylib(s_matherr.o) unused definition of _matherr
/usr/bin/ld: warning unused multiple definitions of symbol _regcomp
../../../../bin/R.bin definition of _regcomp
/usr/lib/libm.dylib(regcomp.o) unused definition of _regcomp
/usr/bin/ld: warning unused multiple definitions of symbol _regerror
../../../../bin/R.bin definition of _regerror
/usr/lib/libm.dylib(regerror.o) unused definition of _regerror
/usr/bin/ld: warning unused multiple definitions of symbol _regexec
../../../../bin/R.bin definition of _regexec
/usr/lib/libm.dylib(regexec.o) unused definition of _regexec
/usr/bin/ld: warning unused multiple definitions of symbol _regfree
../../../../bin/R.bin definition of _regfree
/usr/lib/libm.dylib(regfree.o) unused definition of _regfree
/usr/bin/ld: warning unused multiple definitions of symbol _signgam
../../../../bin/R.bin definition of _signgam
/usr/lib/libm.dylib(s_signgam.o) unused definition of _signgam
make[5]: *** [tcltk.so] Error 1
make[4]: *** [all] Error 2
make[3]: *** [all] Error 1
make[2]: *** [R] Error 1
make[1]: *** [R] Error 1
make: *** [R] Error 1
--
-------------------------
Don MacQueen
dmacq@ucscalumni.com
California, USA
-------------------------