reinit the tree, so we can have metadata

6 files changed, 120 insertions, 0 deletions

diff --git a/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch
new file mode 100644
index 000000000000..dd5aba4f17da
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.7-implicit-dec.patch
@@ -0,0 +1,12 @@
+diff --git a/silly.c b/silly.c
+index 57d07e8..102156a 100644
+--- a/silly.c
++++ b/silly.c
+@@ -13,6 +13,7 @@
+ #include <stdio.h>
+ #include <stdlib.h>
+ #include <math.h>
++#include <string.h>
+ 
+ #ifndef WIN32
+ #include <GL/gl.h>
diff --git a/sci-chemistry/molden/files/molden-4.8-ambfor.patch b/sci-chemistry/molden/files/molden-4.8-ambfor.patch
new file mode 100644
index 000000000000..1ececa7f57e9
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.8-ambfor.patch
@@ -0,0 +1,12 @@
+diff -Naur molden4.8/ambfor/makefile molden4.8.new/ambfor/makefile
+--- molden4.8/ambfor/makefile	2009-12-19 06:14:32.000000000 -0500
++++ molden4.8.new/ambfor/makefile	2010-02-25 22:33:41.000000000 -0500
+@@ -32,7 +32,7 @@
+ 	$(LDR) -o ambmd md.o verlet.o allocmd.o $(OBJS) $(LIBS)
+ 
+ ambfor.o:	ambfor.f
+-	${FC} -c -g -ffast-math -funroll-loops -m32 -o ambfor.o ambfor.f
++	${FC} $(FFLAGS) -c ambfor.f -o ambfor.o 
+ 
+ allocmd.o:	alloc.c
+ 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
diff --git a/sci-chemistry/molden/files/molden-4.8-ldflags.patch b/sci-chemistry/molden/files/molden-4.8-ldflags.patch
new file mode 100644
index 000000000000..92fa6c665f3f
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.8-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/makefile b/makefile
+index 81147a3..9e2353e 100644
+--- a/makefile
++++ b/makefile
+@@ -224,10 +224,10 @@ all:	molden gmolden ambfor/ambfor ambfor/ambmd surf/surf
+ 
+ 
+ molden:	$(OBJS) mpdum.o xwin.o 
+-	$(LDR) -o molden $(OBJS) mpdum.o xwin.o $(LIBS)
++	$(LDR) $(LDFLAGS) -o molden $(OBJS) mpdum.o xwin.o $(LIBS)
+ 
+ gmolden:	$(OBJS) mpdum.o xwingl.o 
+-	$(LDR) -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG)
++	$(LDR) $(LDFLAGS)  -o gmolden $(OBJS) mpdum.o xwingl.o $(LIBSG)
+ 
+ ambfor/ambfor:	ambfor/*.f ambfor/*.c
+ 	$(MAKE) -C ambfor FC=${FC} FFLAGS="${FFLAGS}" LDR="${LDR}" CFLAGS="${CFLAGS}"
+@@ -269,7 +269,7 @@ short_wrl:	short_wrl.o
+ # Moldens OpenGL helper program
+ 
+ moldenogl:	oglmol.o silly.o
+-	$(CC) -o moldenogl oglmol.o silly.o $(LIBSOGL)
++	$(CC) $(LDFLAGS) -o moldenogl oglmol.o silly.o $(LIBSOGL)
+ 
+ # conversion of CADPAC output to molden format
+ 
diff --git a/sci-chemistry/molden/files/molden-4.8-overflow.patch b/sci-chemistry/molden/files/molden-4.8-overflow.patch
new file mode 100644
index 000000000000..7cbd7f436f57
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-4.8-overflow.patch
@@ -0,0 +1,38 @@
+ xwin.c |   10 ++++++----
+ 1 files changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/xwin.c b/xwin.c
+index f395909..092edff 100644
+--- a/xwin.c
++++ b/xwin.c
+@@ -13552,7 +13552,7 @@ void NewActiveStruct()
+ #ifdef CRAY
+     _fcd ztr;
+ #else
+-    char ztr;
++    char ztr[4];
+ #endif
+ #endif
+ 
+@@ -13650,8 +13650,10 @@ void NewActiveStruct()
+ */
+ 	clfpstr->ihashz = 0;
+ #else
+-	strncpy(&ztr,HetAtm[j],3);
+-	parhet_(&j1,&ztr);
++	if (HetAtm[j] != NULL) {
++	   strncpy(ztr,HetAtm[j],3);
++	   parhet_(&j1,ztr);
++	}
+ #endif
+ #endif
+     }
+@@ -27353,7 +27355,7 @@ char *errstr;
+ 	UpdateZME();
+ 	RedrawScroll(&zscroll);
+     }
+-    strcpy(ZMEerr,errstr);
++    strncpy(ZMEerr,errstr,MAXZMEERR);
+     RedrawStatus();
+ }
+ 
diff --git a/sci-chemistry/molden/files/molden-5.0-ambfor.patch b/sci-chemistry/molden/files/molden-5.0-ambfor.patch
new file mode 100644
index 000000000000..9656ff7a79be
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-5.0-ambfor.patch
@@ -0,0 +1,16 @@
+ ambfor/makefile |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/ambfor/makefile b/ambfor/makefile
+index 8627a11..dbc23a1 100644
+--- a/ambfor/makefile
++++ b/ambfor/makefile
+@@ -47,7 +47,7 @@ ambmd:	md.o verlet.o qvdw.o allocmd.o $(OBJS)
+ 	$(LDR) -o ambmd md.o verlet.o qvdw.o allocmd.o $(OBJS) $(LIBS)
+ 
+ ambfor.o:	ambfor.f
+-	${FC} -c -g -ffast-math -funroll-loops -o ambfor.o ambfor.f
++	${FC} $(FFLAGS) -c -o ambfor.o ambfor.f
+ 
+ allocmd.o:	alloc.c
+ 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
diff --git a/sci-chemistry/molden/files/molden-5.0-overflow.patch b/sci-chemistry/molden/files/molden-5.0-overflow.patch
new file mode 100644
index 000000000000..4fc406266935
--- /dev/null
+++ b/sci-chemistry/molden/files/molden-5.0-overflow.patch
@@ -0,0 +1,16 @@
+ xwin.c |   10 ++++++----
+ 1 files changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/xwin.c b/xwin.c
+index f395909..092edff 100644
+--- a/xwin.c
++++ b/xwin.c
+@@ -27353,7 +27355,7 @@ char *errstr;
+ 	UpdateZME();
+ 	RedrawScroll(&zscroll);
+     }
+-    strcpy(ZMEerr,errstr);
++    strncpy(ZMEerr,errstr,MAXZMEERR);
+     RedrawStatus();
+ }
+