[R-SIG-Mac]Problem building 1.5.0 from sources
Jan de Leeuw
deleeuw@stat.ucla.edu
Thu, 16 May 2002 08:55:06 -0700
a. see if libxpg4 is installed by fink. if it is, remove it.
b. start a new shell
c. rebuild tcltk from fink, just to be sure
d. get a fresh R-1.5.0
e. do a configure/make
the regular expression etc warnings are harmless
On Thursday, May 16, 2002, at 06:52 AM, Don MacQueen wrote:
> 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
> -------------------------
> _______________________________________________
> R-SIG-Mac mailing list
> R-SIG-Mac@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac
>
>
===
Jan de Leeuw; Professor and Chair, UCLA Department of Statistics;
US mail: 9432 Boelter Hall, Box 951554, Los Angeles, CA 90095-1554
phone (310)-825-9550; fax (310)-206-5658; email: deleeuw@stat.ucla.edu
homepage: http://www.stat.ucla.edu/~deleeuw
========================================================
No matter where you go, there you are. --- Buckaroo Banzai
http://www.stat.ucla.edu/~deleeuw/sounds/nomatter.au
========================================================