ggobi and Mac OS X
There is no malloc.h in OS X. All the defs are in stdlib.h. If you want to you could make a softlink /usr/local/inlcude/malloc.h to /usr/include/stdlib.h, or even make a dummy empty malloc.h.
On Wednesday, Mar 19, 2003, at 11:33 US/Pacific, 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@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@stat.math.ethz.ch wrote:
Date: Tue, 18 Mar 2003 10:27:01 -0800 From: Jan de Leeuw <deleeuw@stat.ucla.edu> Subject: Re: [R-SIG-Mac]ggobi and Mac OS X To: "Dennis A. Wolf" <wolfda@ornl.gov> Cc: r-sig-mac@stat.math.ethz.ch Message-ID: <35DD2522-596F-11D7-91B1-000393860F3C@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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=== Jan de Leeuw; Professor and Chair, UCLA Department of Statistics; Editor: Journal of Multivariate Analysis, Journal of Statistical Software 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://gifi.stat.ucla.edu ------------------------------------------------------------------------ ------------------------- No matter where you go, there you are. --- Buckaroo Banzai http://gifi.stat.ucla.edu/sounds/nomatter.au ------------------------------------------------------------------------ -------------------------