Update of /cvsroot/fink/dists/10.3/unstable/main/finkinfo/sci In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17600/10.3/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/10.3/unstable/main/finkinfo/sci/gopenmol.patch,v retrieving revision 1.1 retrieving revision 1.2 diff -u -d -r1.1 -r1.2 --- gopenmol.patch 13 May 2004 18:10:25 -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 ------------------------------------------------------- Using Tomcat but need to do more? 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