[R-SIG-Mac]Re: ggobi and Mac OS X

Wed Mar 19 14:33:12 MET 2003

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.
>>
>> _______________________________________________
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>> R-SIG-Mac at stat.math.ethz.ch
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>>
>>