[R-SIG-Mac]Re: ggobi and Mac OS X
Dennis A. Wolf
wolfda at ornl.gov
Wed Mar 19 15:57:34 MET 2003
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?
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
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>
> --
> _______________________________________________________________
>
> 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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