Update of /cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci
In directory
sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17600/10.4-transitional/unstable/main/finkinfo/sci
Modified Files:
gopenmol.patch
Log Message:
Build cleanups; move headers into new -dev splitoff; disable icon8; switch to
freeglut
Index: gopenmol.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.4-transitional/unstable/main/finkinfo/sci/gopenmol.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- gopenmol.patch 27 Apr 2005 03:26:22 -0000 1.1
+++ gopenmol.patch 3 May 2006 07:55:49 -0000 1.2
@@ -47,6 +47,18 @@
}
}
+diff -Nurd -x'*~' gOpenMol-2.30.orig/density/density.c
gOpenMol-2.30/density/density.c
+--- gOpenMol-2.30.orig/density/density.c 2003-05-19 13:24:12.000000000
-0400
++++ gOpenMol-2.30/density/density.c 2006-05-02 17:35:16.000000000 -0400
+@@ -12,7 +12,7 @@
+ #include <math.h>
+ #include <string.h>
+ #include <sys/types.h>
+-#include <malloc.h>
++#include <stdlib.h>
+
+ #define VERBOSE 0
+ #define BUFF_LEN 500
diff -Nurd -x'*~' gOpenMol-2.30.orig/src/config.mk.ac
gOpenMol-2.30/src/config.mk.ac
--- gOpenMol-2.30.orig/src/config.mk.ac 2003-09-17 05:58:43.000000000
-0400
+++ gOpenMol-2.30/src/config.mk.ac 2003-10-15 19:08:53.000000000 -0400
@@ -89,6 +101,18 @@
# Check for the library.
gom4_GOM_CHECK_LIB_found=yes
for gom4_GOM_CHECK_LIB_header in tcl.h
+diff -Nurd -x'*~' gOpenMol-2.30.orig/src/general/math_oper.c
gOpenMol-2.30/src/general/math_oper.c
+--- gOpenMol-2.30.orig/src/general/math_oper.c 2003-07-29 05:22:25.000000000
-0400
++++ gOpenMol-2.30/src/general/math_oper.c 2006-05-02 17:22:37.000000000
-0400
+@@ -13,7 +13,7 @@
+
+ #include <float.h>
+ #include <math.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <stdio.h>
+
+ #include "gommain.h"
diff -Nurd -x'*~' gOpenMol-2.30.orig/src/general/trajectory.c
gOpenMol-2.30/src/general/trajectory.c
--- gOpenMol-2.30.orig/src/general/trajectory.c 2003-09-09
08:49:05.000000000 -0400
+++ gOpenMol-2.30/src/general/trajectory.c 2003-10-15 19:08:53.000000000
-0400
@@ -153,16 +177,27 @@
/*************************************************************************/
int gomp_SetVelocityMinMax(float Vmin , float Vmax)
/*************************************************************************/
+diff -Nurd -x'*~' gOpenMol-2.30.orig/src/general/utility4.c
gOpenMol-2.30/src/general/utility4.c
+--- gOpenMol-2.30.orig/src/general/utility4.c 2003-07-31 05:29:36.000000000
-0400
++++ gOpenMol-2.30/src/general/utility4.c 2006-05-02 17:22:08.000000000
-0400
+@@ -26,7 +26,7 @@
+ #include <sys/resource.h>
+ #endif
+
+-#include <malloc.h>
++#include <stdlib.h>
+
+ #if defined(IRIX)
+ #include <sys/procfs.h>
diff -Nurd -x'*~' gOpenMol-2.30.orig/src/include/memalloc.h
gOpenMol-2.30/src/include/memalloc.h
--- gOpenMol-2.30.orig/src/include/memalloc.h 2003-07-29 05:22:51.000000000
-0400
-+++ gOpenMol-2.30/src/include/memalloc.h 2003-10-15 19:08:53.000000000
-0400
-@@ -16,6 +16,9 @@
++++ gOpenMol-2.30/src/include/memalloc.h 2006-05-02 17:23:28.000000000
-0400
+@@ -15,7 +15,7 @@
+ #ifndef INC_GOPENMOL_MEMALLOC
#define INC_GOPENMOL_MEMALLOC
- #include <malloc.h>
-+#if HAVE_STDLIB_H
+-#include <malloc.h>
+#include <stdlib.h>
-+#endif
extern float *gomp_Fvector(int);
extern double *gomp_Dvector(int);
@@ -181,6 +216,17 @@
static const IntFunc parseShowAtomIdentify = { gomp_GetIdentifyAtomActive };
/* show atom selection */
+diff -Nurd -x'*~' gOpenMol-2.30.orig/src/plugins/ball/ball.c
gOpenMol-2.30/src/plugins/ball/ball.c
+--- gOpenMol-2.30.orig/src/plugins/ball/ball.c 2003-08-05 08:29:18.000000000
-0400
++++ gOpenMol-2.30/src/plugins/ball/ball.c 2006-05-02 17:30:13.000000000
-0400
+@@ -1,6 +1,6 @@
+ #include <tcl.h>
+ #include <assert.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <stdio.h>
+
+ #ifdef WIN32
diff -Nurd -x'*~' gOpenMol-2.30.orig/src/plugins/config.mk.ac
gOpenMol-2.30/src/plugins/config.mk.ac
--- gOpenMol-2.30.orig/src/plugins/config.mk.ac 2003-09-12
05:25:41.000000000 -0400
+++ gOpenMol-2.30/src/plugins/config.mk.ac 2003-10-15 19:08:53.000000000
-0400
@@ -217,6 +263,42 @@
::lulUpdatePluginsMenu
}
+diff -Nurd -x'*~' gOpenMol-2.30.orig/src/readwrite/rw_get_frame_gromacs.c
gOpenMol-2.30/src/readwrite/rw_get_frame_gromacs.c
+--- gOpenMol-2.30.orig/src/readwrite/rw_get_frame_gromacs.c 2003-07-29
05:23:49.000000000 -0400
++++ gOpenMol-2.30/src/readwrite/rw_get_frame_gromacs.c 2006-05-02
17:26:21.000000000 -0400
+@@ -22,7 +22,7 @@
+
+ #include <stdio.h>
+ #include <math.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <string.h>
+ #include <tcl.h>
+
+diff -Nurd -x'*~' gOpenMol-2.30.orig/src/readwrite/rw_gotosgi.c
gOpenMol-2.30/src/readwrite/rw_gotosgi.c
+--- gOpenMol-2.30.orig/src/readwrite/rw_gotosgi.c 2003-08-06
03:42:41.000000000 -0400
++++ gOpenMol-2.30/src/readwrite/rw_gotosgi.c 2006-05-02 17:27:26.000000000
-0400
+@@ -22,7 +22,7 @@
+ #include "maindefs.h"
+
+ #include <stdio.h>
+-#include <malloc.h>
++#include <stdlib.h>
+
+ #include "gomimage.h"
+ #include "pbmplus_x.h"
+diff -Nurd -x'*~' gOpenMol-2.30.orig/src/readwrite/rw_read_gbl_input.c
gOpenMol-2.30/src/readwrite/rw_read_gbl_input.c
+--- gOpenMol-2.30.orig/src/readwrite/rw_read_gbl_input.c 2003-07-31
05:30:33.000000000 -0400
++++ gOpenMol-2.30/src/readwrite/rw_read_gbl_input.c 2006-05-02
17:28:09.000000000 -0400
+@@ -16,7 +16,7 @@
+ #include <string.h>
+ #include <ctype.h>
+ #include <sys/types.h>
+-#include <malloc.h>
++#include <stdlib.h>
+
+ #if defined(IRIX)
+ #include <bstring.h>
diff -Nurd -x'*~' gOpenMol-2.30.orig/src/readwrite/rw_rforce.c
gOpenMol-2.30/src/readwrite/rw_rforce.c
--- gOpenMol-2.30.orig/src/readwrite/rw_rforce.c 2003-07-29
05:23:51.000000000 -0400
+++ gOpenMol-2.30/src/readwrite/rw_rforce.c 2003-10-15 19:08:53.000000000
-0400
@@ -229,6 +311,18 @@
/*************************************************************************/
int gomp_GetVectorStructureIndex()
/*************************************************************************/
+diff -Nurd -x'*~' gOpenMol-2.30.orig/src/readwrite/rw_rmopac.c
gOpenMol-2.30/src/readwrite/rw_rmopac.c
+--- gOpenMol-2.30.orig/src/readwrite/rw_rmopac.c 2003-07-29
05:23:51.000000000 -0400
++++ gOpenMol-2.30/src/readwrite/rw_rmopac.c 2006-05-02 17:29:14.000000000
-0400
+@@ -42,7 +42,7 @@
+ #include <math.h>
+ #include <string.h>
+ #include <ctype.h>
+-#include <malloc.h>
++#include <stdlib.h>
+
+ #include "coord_file.h"
+ #include "molecule.h"
diff -Nurd -x'*~' gOpenMol-2.30.orig/src/unix/data/environment.txt
gOpenMol-2.30/src/unix/data/environment.txt
--- gOpenMol-2.30.orig/src/unix/data/environment.txt 2003-08-05
08:33:27.000000000 -0400
+++ gOpenMol-2.30/src/unix/data/environment.txt 2003-10-15
19:08:53.000000000 -0400
@@ -321,31 +415,18 @@
install-plugins: FORCE
diff -Nurd -x'*~' gOpenMol-2.30.orig/src/unix/make/utility.mk.ac
gOpenMol-2.30/src/unix/make/utility.mk.ac
--- gOpenMol-2.30.orig/src/unix/make/utility.mk.ac 2003-09-17
05:58:53.000000000 -0400
-+++ gOpenMol-2.30/src/unix/make/utility.mk.ac 2003-10-15 19:08:53.000000000
-0400
-@@ -20,7 +20,7 @@
-
- OBJECTS_C = fmalloc.o
-
--BINARIES = $(BINARIES_C) $(BINARIES_CXX) $(BINARIES_F) $(BINARIES_JAR)
-+BINARIES = $(BINARIES_C) $(BINARIES_CXX) $(BINARIES_F) $(BINARIES_JAR)
$(BINARIES_SPECIAL)
-
- BINARIES_C = contman$(EXEEXT) \
- g94cub2pl$(EXEEXT) \
-@@ -47,8 +47,11 @@
++++ gOpenMol-2.30/src/unix/make/utility.mk.ac 2006-05-03 02:19:35.000000000
-0400
+@@ -47,8 +47,7 @@
xmol2bamber$(EXEEXT) \
xplor2charmm$(EXEEXT) \
gridasc2plt$(EXEEXT) \
- gridbin2plt$(EXEEXT) \
- icon8$(EXEEXT)
+ gridbin2plt$(EXEEXT)
-+
-+BINARIES_SPECIAL = $(BINARIES_icon8)
-+
-+BINARIES_icon8 = icon8$(EXEEXT)
BINARIES_JAR = xvibs.jar
-@@ -75,13 +78,16 @@
+@@ -75,10 +74,10 @@
$(LIBTOOL) --tag=CC --tag=disable-shared --mode=compile $(CC) -c -o $@
$^
$(BINARIES_C):
@@ -357,17 +438,19 @@
+ $(CXX) -o $@ $^ $(LDFLAGS) $(UTIL_LIBS)
$(BINARIES_F):
-- $(F77) -o $@ $^ $(UTIL_LIBS)
-+ $(F77) -ffixed-line-length-none -o $@ $^ $(UTIL_LIBS)
-+
-+$(BINARIES_icon8):
-+ $(F77) -ffixed-line-length-none -fno-globals -o $@ $^ $(UTIL_LIBS)
-
- $(BINARIES_JAR):
- cp $^ $@
+ $(F77) -o $@ $^ $(UTIL_LIBS)
diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/UHBD/gridasc2plt.f
gOpenMol-2.30/utility/UHBD/gridasc2plt.f
--- gOpenMol-2.30.orig/utility/UHBD/gridasc2plt.f 2003-05-19
13:24:53.000000000 -0400
-+++ gOpenMol-2.30/utility/UHBD/gridasc2plt.f 2003-10-15 19:08:53.000000000
-0400
++++ gOpenMol-2.30/utility/UHBD/gridasc2plt.f 2006-05-02 18:17:09.000000000
-0400
+@@ -24,7 +24,7 @@
+ end do
+ end do
+
+- write(6,*) 'I assume ascii uhbd output; must be 200x200x200 or less'
++ write(6,*) 'I assume ascii uhbd output; maximum 200x200x200'
+ 100 continue
+ write(6,*) 'UHBD .phi grid file name:'
+ read (5,991) uhbdfile
@@ -32,7 +32,7 @@
read (5,991) pltfile
991 format (a80)
@@ -379,7 +462,16 @@
78 format(3i7)
diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/UHBD/gridbin2plt.f
gOpenMol-2.30/utility/UHBD/gridbin2plt.f
--- gOpenMol-2.30.orig/utility/UHBD/gridbin2plt.f 2003-05-19
13:24:54.000000000 -0400
-+++ gOpenMol-2.30/utility/UHBD/gridbin2plt.f 2003-10-15 19:08:53.000000000
-0400
++++ gOpenMol-2.30/utility/UHBD/gridbin2plt.f 2006-05-02 18:17:00.000000000
-0400
+@@ -15,7 +15,7 @@
+ integer im,jm,km,idum1,idum2,idum3,idum4,grdflg,kdum1,kdum2
+ real dum2,dum3,dum4,dum5,dum6,dum7,dum8
+
+- write(6,*) 'I assume binary uhbd output; must be 200x200x200 or less'
++ write(6,*) 'I assume binary uhbd output; maximum 200x200x200'
+ 100 continue
+ write(6,*) 'UHBD .phi grid file name:'
+ read (5,991) uhbdfile
@@ -23,7 +23,7 @@
read (5,991) pltfile
991 format (a80)
@@ -401,3 +493,63 @@
End if
*
C ATOMS
+diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/g94cub2pl.c
gOpenMol-2.30/utility/g94cub2pl.c
+--- gOpenMol-2.30.orig/utility/g94cub2pl.c 2003-07-28 06:39:06.000000000
-0400
++++ gOpenMol-2.30/utility/g94cub2pl.c 2006-05-02 17:32:35.000000000 -0400
+@@ -313,7 +313,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <sys/types.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <string.h>
+
+ #define BUFF_LEN 256
+diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/gamess2plt.c
gOpenMol-2.30/utility/gamess2plt.c
+--- gOpenMol-2.30.orig/utility/gamess2plt.c 2003-05-19 13:24:51.000000000
-0400
++++ gOpenMol-2.30/utility/gamess2plt.c 2006-05-02 17:33:12.000000000 -0400
+@@ -84,7 +84,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <sys/types.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <string.h>
+
+ #define BUFF_LEN 256
+diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/gcube2plt.c
gOpenMol-2.30/utility/gcube2plt.c
+--- gOpenMol-2.30.orig/utility/gcube2plt.c 2003-07-28 06:39:07.000000000
-0400
++++ gOpenMol-2.30/utility/gcube2plt.c 2006-05-02 17:33:55.000000000 -0400
+@@ -304,7 +304,7 @@
+ #include <math.h>
+ #include <ctype.h>
+ #include <sys/types.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <string.h>
+
+ #define BUFF_LEN 256
+diff -Nurd -x'*~' gOpenMol-2.30.orig/utility/jaguar2plt.c
gOpenMol-2.30/utility/jaguar2plt.c
+--- gOpenMol-2.30.orig/utility/jaguar2plt.c 2003-05-19 13:24:52.000000000
-0400
++++ gOpenMol-2.30/utility/jaguar2plt.c 2006-05-02 17:34:35.000000000 -0400
+@@ -24,7 +24,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <sys/types.h>
+-#include <malloc.h>
++#include <stdlib.h>
+ #include <string.h>
+
+ #define BUFF_LEN 256
+diff -Nurd -x'*~' gOpenMol-2.30.orig/vss/vssmod.c gOpenMol-2.30/vss/vssmod.c
+--- gOpenMol-2.30.orig/vss/vssmod.c 2003-05-19 13:24:54.000000000 -0400
++++ gOpenMol-2.30/vss/vssmod.c 2006-05-02 17:35:50.000000000 -0400
+@@ -19,7 +19,7 @@
+ #include <stdio.h>
+ #include <math.h>
+ #include <string.h>
+-#include <malloc.h>
++#include <stdlib.h>
+
+ #define LINE_LEN 80
+ #define BUFF_LEN 500
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