These are the things that are patched AFTER applying the Jaguar Patch


ss/parse.c
**********

line 96:
Problem with gcc 3.4, error because of old style c++. "int" added before the function name to declare the return type. Declaration "int PTFree()" removed from function block


Makefile
********

line 167 ... : 
activate sprng random generato

line 969 :
Because of some parsing errors I removed the "-traditional-cpp" flag


Makefile.MacOSXDarwin
*********************
line 24:
Use ranlib, so "@echo no ranlib for" by "$(RANLIB_IN)"



Xodus/Widg/Text.c
*****************
line 63: 
include stdarg.h instead of varargs.h

line 140:
with stdarg.h all the arguments of the function have to be declared:
"CallAction()" replaced by "CallAction(void (*action) (), Widget widget, XEvent *event, ... )"

line 290:
compiler gives a cast error. "tnew" replaced by "(Widget)tnew"

line 325:
same as line 290

line 666:
"static void
CallAction(action, widget, event, va_alist)
       void            (*action) ();
       Widget          widget;
       XEvent         *event;
va_dcl" 
replaced by
"CallAction(void (*action) (), Widget widget, XEvent *event, ... )"

and "va_start(args)" by "va_start(args,event)"



Xodus/Xo/Error.c
Xodus/Xo/XoArgsLists.c
diskio/diskio_func_ext.h
diskio/diskio_utilfunc.c
shell/shell_log.c
************************

are all adapted to use stdarg.h instead of varargs.h by changing the declarations of the functions that these headers and by replacing va_start(args) by va_start(args,"the argument before the ...")




diskio/interface/netcdf/netcdf-3.4/src/config.log
diskio/interface/netcdf/netcdf-3.4/src/config.status
****************************************************

these files are removed
("Make clean" doesn't seem to do this) 


diskio/interface/netcdf/netcdf-3.4/src/libsrc/ncconfig.h
********************************************************

line 44:
#define HAVE_ALLOCA_H 1 added


diskio/interface/netcdf/netcdf-3.4/src/ncgen/ncgentab.c
*******************************************************
line 81:
sys/types.h included



kinetics/enz.c 
kinetics/ksolve.c
kinetics/pool.c
kinetics/reac.c
***************
In every of these files the "return(1)" statement is added at the end of a CREATE action (Older compilers returned the data that was on the stack when there was no "return" statement. But now it looks that gcc always returns "0" and this gives problems because this return value is used as an indication of errors.


liblist
minliblist
**********
are removed

param/param_defs.h 

line 100 ...:
the indention is removed



shell/shell.h
*************
line 17:
"#if defined(" replaced by "#ifdef"



src/sprng/Makefile
******************
line 39:
problem with "all: src", because the Mac OS X disks are not case sensitive, "make" thinks that "src" is the same as "SRC" and it tries to "make" the directory "SRC" which fails. So I renamed "src" to "source" 


sprng/SRC/make.MacOSXDarwin
***************************
line 31:
the include directory should be "/usr/include" (because otherwise the wrong time.h is included) and the "-traditional-cpp" is removed from the CFLAGS



********************************
Only for GENESIS 2.2.1 (not 2.2)
********************************
kinetics/Makefile
*****************

line 88:
"-I$(XINCLUDE)" added to CFLAGS, because now X is used.

kinetics/enz.c
src/kinetics/gsolve.c
**************
The function "G_RNG()" is used in stead of "sprng()" because that way it is possible to let genesis decide which random generator is used.


kinetics/file_info.c
********************
Creation of a new function: "alphsort" (no spelling mistake) because "alphasort" is not available anymore from the libraries