[R-SIG-Mac]Re: ggobi and Mac OS X
Duncan Temple Lang
duncan at research.bell-labs.com
Wed Mar 19 18:00:55 MET 2003
Dennis A. Wolf wrote:
> Thanks very much for your help. I am getting further along in the
> process with your help and the readme link. However, I don't know what
> to do about the values.h missing. In the README.OSX file it says:
>
> The inclusion of values.h in utils.c causes problems also.
> We can conditionally include this with the pre-processor
> symbol
> -DNO_VALUES_H
>
> How do I use this symbol?
Good question; my notes in README.OSX were more notes to me than
instructions for others! Sorry about that.
You can typically include -DNO_VALUES_H in the value of CFLAGS which
is used when compiling the .o from a .c file. Until I fix the
configuration to deal with the Mac, you might add this to PIC_CFLAG in
the Makeconf (or Makeconf.in).
Thanks for your patience. I do hope to get to all of this later in the
week (i.e. tomorrow or Friday) as I also am dealing with plugins on
Windows for GGobi. So it is all related!
D.
>
> Thanks again!
> --Dennis Wolf
>
> On Wednesday, Mar 19, 2003, at 15:29 US/Eastern, Duncan Temple Lang
> wrote:
>
> >
> > There is hopefully a file named README.OSX in the distribution
> > that provides some (few) hints about compiling on OSX. It may not
> > get added to the tar file when I build the distribution.
> > You can find it at
> > http://www.ggobi.org/README.OSX
> >
> > Anyway, in there, I suggest just creating malloc.h locally
> > within the GGobi source files as an empty file.
> >
> > D.
> >
> >
> > Dennis A. Wolf wrote:
> >> I looked around in the Makeconf file in R and found
> >>
> >> SHLIB_LDFLAGS= -bundle -flat_namespace -undefined suppress
> >>
> >> I edited the Makeconf that was created when ggobi was configured and
> >> replaced -shared with the above. The error I got was
> >>
> >> tour_pp.c:31: header file 'malloc.h' not found
> >>
> >> Does this have anything to do with the revised flags? Any suggestions
> >> on how to proceed?
> >>
> >> Thanks!
> >>
> >> Dennis A. Wolf, Ph.D.
> >> Computer Sciences and Mathematics Division
> >> Oak Ridge National Laboratory
> >> POB 2008, Building 6011, MS 6418
> >> Oak Ridge, TN 37831-6418
> >>
> >> phone: (865) 574-6326
> >> fax: (865) 576-3513
> >> email: wolfda at ornl.gov
> >>
> >> The full details from configure and make are:
> >> qedmac 1106> sudo ./configure --with-xml --with-R --enable-embed
> >> loading cache ./config.cache
> >> checking for gtk-config... (cached) /sw/bin/gtk-config
> >> Setting gtk flags
> >> checking for uname... (cached) /usr/bin/uname
> >> checking for install... (cached) /usr/bin/install
> >> checking for gcc... (cached) gcc
> >> checking whether the C compiler (gcc ) works... yes
> >> checking whether the C compiler (gcc ) is a cross-compiler... no
> >> checking whether we are using GNU C... (cached) yes
> >> checking whether gcc accepts -g... (cached) yes
> >> Checking flag for linking shared libraries
> >> SHLIB linker flags: -shared
> >> with_xml: yes
> >> checking for xml2-config... (cached) /sw/bin/xml2-config
> >> Have xml-config: /sw/bin/xml2-config
> >> USE_XML := USE_XML=2
> >> XML Version := 2
> >> checking for R... (cached) /usr/local/bin/R
> >> checking for uname... (cached) /usr/bin/uname
> >> creating ./config.status
> >> creating Makeconf
> >> creating GNUmakefile
> >> creating src/GNUmakefile
> >> creating gtkext/src/GNUmakefile
> >> creating bin/setLD.csh
> >> creating bin/setLD.bsh
> >> creating bin/ggobi
> >> creating bin/ggobi-config
> >> creating bugTemplate
> >> creating share/ggobirc
> >> creating local.config
> >> creating share/tools/plugin
> >> creating src/config.h
> >> src/config.h is unchanged
> >> Installation directory: /usr/local
> >> qedmac 1107> sudo vi Makeconf
> >> qedmac 1108> sudo make
> >> make -C src ../bin/ggobi.bin
> >> gcc -I../include -I../gtkext/include -I/sw/include/gtk-1.2
> >> -I/sw/include/glib-1.2 -I/sw/lib/glib/include -I/usr/X11R6/include
> >> -I/sw/include/libxml2 -I/sw/include -DUSE_XML=2 -DSUPPORT_PLUGINS=1
> >> -DSUPPORT_INIT_FILES=1 -DHAVE_CONFIG_H -c tour_pp.c -o tour_pp.o
> >> tour_pp.c:31: header file 'malloc.h' not found
> >> cpp-precomp: warning: errors during smart preprocessing, retrying in
> >> basic mode
> >> make[1]: *** [tour_pp.o] Error 1
> >> make: *** [bin/ggobi.bin] Error 2
> >>
> >>
> >> On Wednesday, Mar 19, 2003, at 06:01 US/Eastern,
> >> r-sig-mac-request at stat.math.ethz.ch wrote:
> >>> Date: Tue, 18 Mar 2003 10:27:01 -0800
> >>> From: Jan de Leeuw <deleeuw at stat.ucla.edu>
> >>> Subject: Re: [R-SIG-Mac]ggobi and Mac OS X
> >>> To: "Dennis A. Wolf" <wolfda at ornl.gov>
> >>> Cc: r-sig-mac at stat.math.ethz.ch
> >>> Message-ID: <35DD2522-596F-11D7-91B1-000393860F3C at stat.ucla.edu>
> >>> Content-Type: text/plain; charset=US-ASCII; format=flowed
> >>>
> >>> In MacOS X you can build either dynamic libraries (foo.dylib), which
> >>> are
> >>> to be linked against, or bundles (foo.so) which are to be loaded at
> >>> run
> >>> time (plugins, packages). Most ELF based systems dont distinguish the
> >>> two.
> >>>
> >>> So in R, for instance, you make libR.dylib and R_gnome.so or
> >>> tcltk.so.
> >>> For dylibs you need the flag -dynamiclib, for bundles you need
> >>> -bundle
> >>> (but more, because you need to tell the linker what to do about
> >>> undefined
> >>> symbols). See the configure files for R for more details.
> >>>
> >>> I'll look at ggobi, which I have running, but I am not sure what I
> >>> needed
> >>> to do.
> >>>
> >>> On Tuesday, March 18, 2003, at 08:35 AM, Dennis A. Wolf wrote:
> >>>
> >>>> Greetings:
> >>>>
> >>>> I have been trying to install ggobi with the ultimate goal of using
> >>>> it
> >>>> within R. I am having difficulty which appears to be related to gcc
> >>>> not allowing -shared as an option with Mac OS X. Can anyone suggest
> >>>> how I can overcome this problem?
> >>>>
> >>>> I am using a 15" flat-panel iMac, Mac OSX 10.2.4, Apple's X11 beta
> >>>> 3.
> >>>>
> >>>> The gory details of the attempted installation follow:
> >>>>
> >>>> I downloaded ggobi, ggobi_0.99-10.tar.gz and gunzipped and tarred it
> >>>> as su to get the directory /usr/local/lib/ggobi and within that
> >>>> directory I did
> >>>>
> >>>> sudo ./configure --with-xml --enable-embed
> >>>>
> >>>> and got:
> >>>>
> >>>> loading cache ./config.cache
> >>>> checking for gtk-config... (cached) /sw/bin/gtk-config
> >>>> Setting gtk flags
> >>>> checking for uname... (cached) /usr/bin/uname
> >>>> checking for install... (cached) /usr/bin/install
> >>>> checking for gcc... (cached) gcc
> >>>> checking whether the C compiler (gcc ) works... yes
> >>>> checking whether the C compiler (gcc ) is a cross-compiler... no
> >>>> checking whether we are using GNU C... (cached) yes
> >>>> checking whether gcc accepts -g... (cached) yes
> >>>> Checking flag for linking shared libraries
> >>>> SHLIB linker flags: -shared
> >>>> with_xml: yes
> >>>> checking for xml2-config... (cached) /sw/bin/xml2-config
> >>>> Have xml-config: /sw/bin/xml2-config
> >>>> USE_XML := USE_XML=2
> >>>> XML Version := 2
> >>>> checking for uname... (cached) /usr/bin/uname
> >>>> creating ./config.status
> >>>> creating Makeconf
> >>>> creating GNUmakefile
> >>>> creating src/GNUmakefile
> >>>> creating gtkext/src/GNUmakefile
> >>>> creating bin/setLD.csh
> >>>> creating bin/setLD.bsh
> >>>> creating bin/ggobi
> >>>> creating bin/ggobi-config
> >>>> creating bugTemplate
> >>>> creating share/ggobirc
> >>>> creating local.config
> >>>> creating share/tools/plugin
> >>>> creating src/config.h
> >>>> src/config.h is unchanged
> >>>> Installation directory: /usr/local
> >>>>
> >>>> Now when I
> >>>>
> >>>> sudo make
> >>>>
> >>>> I got
> >>>>
> >>>> make -C gtkext/src install
> >>>> gcc -shared -o libgtkext.so cokus.lo mt19937ar.lo gtkextruler.lo
> >>>> gtkexthruler.lo gtkextvruler.lo
> >>>> gcc: unrecognized option `-shared'
> >>>> ld: Undefined symbols:
> >>>> _main
> >>>> _g_log
> >>>> _gdk_draw_pixmap
> >>>> _gdk_gc_destroy
> >>>> _gdk_gc_new
> >>>> _gdk_gc_set_exposures
> >>>> _gdk_pixmap_new
> >>>> _gdk_pixmap_unref
> >>>> _gdk_window_get_size
> >>>> _gdk_window_move_resize
> >>>> _gdk_window_new
> >>>> _gdk_window_set_user_data
> >>>> _gtk_marshal_NONE__NONE
> >>>> _gtk_object_class_add_signals
> >>>> _gtk_signal_new
> >>>> _gtk_style_attach
> >>>> _gtk_style_set_background
> >>>> _gtk_type_check_class_cast
> >>>> _gtk_type_check_object_cast
> >>>> _gtk_type_class
> >>>> _gtk_type_is_a
> >>>> _gtk_type_unique
> >>>> _gtk_widget_get_colormap
> >>>> _gtk_widget_get_events
> >>>> _gtk_widget_get_parent_window
> >>>> _gtk_widget_get_type
> >>>> _gtk_widget_get_visual
> >>>> _gtk_widget_queue_draw
> >>>> _gtk_widget_set_state
> >>>> _myrint
> >>>> _gdk_draw_line
> >>>> _gdk_draw_string
> >>>> _gdk_pointer_grab
> >>>> _gdk_pointer_ungrab
> >>>> _gdk_window_get_pointer
> >>>> _gtk_paint_box
> >>>> _gtk_signal_emit_by_name
> >>>> _gtk_type_new
> >>>> make[1]: *** [libgtkext.so] Error 1
> >>>> make: *** [lib/libgtkext.so] Error 2
> >>>>
> >>>> It appears that gcc does not like the -shared option. And indeed in
> >>>> the help file for gcc it says that this option is not allowed for
> >>>> Mac
> >>>> OS X.
> >>>>
> >>>> _______________________________________________
> >>>> R-SIG-Mac mailing list
> >>>> R-SIG-Mac at stat.math.ethz.ch
> >>>> https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac
> >>>>
> >>>>
> >>
> >> _______________________________________________
> >> R-SIG-Mac mailing list
> >> R-SIG-Mac at stat.math.ethz.ch
> >> https://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac
> >
> > --
> > _______________________________________________________________
> >
> > Duncan Temple Lang duncan at research.bell-labs.com
> > Bell Labs, Lucent Technologies office: (908)582-3217
> > 700 Mountain Avenue, Room 2C-259 fax: (908)582-3340
> > Murray Hill, NJ 07974-2070
> > http://cm.bell-labs.com/stat/duncan
> >
>
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