biology/molden: Unbreak build; Correct WWW

For unbreak:
- pass FFLAGS to the build
- fix several errors in C
- remove the failing 'ex' command from makefile

Reported by:	fallout
Approved by:	portmgr (unbreak)

5 files changed, 86 insertions, 1 deletions

diff --git a/biology/molden/files/patch-makefile b/biology/molden/files/patch-makefile
new file mode 100644
index 000000000000..4a086a6fdd57
--- /dev/null
+++ b/biology/molden/files/patch-makefile
@@ -0,0 +1,41 @@
+- pass supplied FFLAGS to the build
+
+--- makefile.orig	2021-01-28 14:05:10 UTC
++++ makefile
+@@ -107,7 +107,7 @@ ifneq ($(comgcc), $(empty))
+    EXTRAZ = -Wno-implicit-function-declaration
+    EXT = ${EXTRAZ}
+ endif
+-FFLAGS = -g ${AFLAG}
++FFLAGS += -g ${AFLAG}
+ LIBS =  -L/usr/X11R6/lib -lX11 -lm
+ ifeq ($(AFLAG),"-m64")
+ LIBS =  -L/usr/X11R6/lib64 -lX11 -lm
+@@ -132,11 +132,11 @@ ifeq ($(uname), Darwin)
+ #
+ CC=cc
+ CFLAGS= -std=gnu89 -Wno-return-type -DDARWIN -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -Wno-logical-op-parentheses
+-FFLAGS=-O3 -funroll-loops
++FFLAGS+=-O3 -funroll-loops
+ LIBS = -L/usr/X11R6/lib -lX11 -lm
+ LIBSG = -L/usr/X11R6/lib -lGLU "-Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -lGL -lXmu -lX11 -lm
+ EXT= -std=gnu89 -Wno-return-type -DDARWIN ${EXTRAZ}
+-FFLAGS=-O3 -funroll-loops
++FFLAGS+=-O3 -funroll-loops
+ LIBS = -L/usr/X11R6/lib -lX11 -lm
+ LIBSG = -L/usr/X11R6/lib -lGLU "-Wl,-dylib_file,/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" -lGL -lXmu -lX11 -lm
+ CFLAGS= -g -std=gnu89 -Wno-return-type -DDARWIN -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 -Wno-logical-op-parentheses -Wno-implicit-function-declaration -Wno-tautological-pointer-compare -Wno-tautological-constant-out-of-range-compare
+@@ -306,11 +306,11 @@ gmolden:	$(OBJS) src/mpdum.o src/xwingl.o 
+ 	mv gmolden bin/gmolden
+ 
+ ambfor/ambfor:	src/ambfor/*.f src/ambfor/*.c
+-	$(MAKE) -C src/ambfor FC=${FC} LDR="${LDR}" EXT="${EXT}"
++	$(MAKE) -C src/ambfor FC=${FC} LDR="${LDR}" EXT="${EXT}" FFLAGS="$(FFLAGS)"
+ 	mv src/ambfor/ambfor bin/ambfor
+ 
+ ambfor/ambmd:	src/ambfor/*.f src/ambfor/*.c
+-	$(MAKE) -C src/ambfor ambmd FC=${FC} LDR="${LDR}" EXT="${EXT}"
++	$(MAKE) -C src/ambfor ambmd FC=${FC} LDR="${LDR}" EXT="${EXT}" FFLAGS="$(FFLAGS)" FFLAGS="$(FFLAGS)"
+ 	mv src/ambfor/ambmd bin/ambmd
+ 
+ surf/surf:	src/surf/*.h src/surf/*.c
diff --git a/biology/molden/files/patch-src_surf_Makefile b/biology/molden/files/patch-src_surf_Makefile
new file mode 100644
index 000000000000..ca1673d9c3cf
--- /dev/null
+++ b/biology/molden/files/patch-src_surf_Makefile
@@ -0,0 +1,13 @@
+- disable ex: it breaks the build, not sure why is it there
+
+--- src/surf/Makefile.orig	2022-07-15 23:19:54 UTC
++++ src/surf/Makefile
+@@ -58,7 +58,7 @@ depend: $(DEPEND)
+ 	@ echo '$$r makedep' >>eddep
+ 	@ echo 'w' >>eddep
+ 	@ cp Makefile Makefile.bak
+-	@ ex - Makefile < eddep
++	#@ ex - Makefile < eddep
+ 	@ rm eddep makedep 
+ 	@ echo '  ' >> Makefile
+ 	@ echo '# DEPENDENCIES MUST END AT END OF FILE' >> Makefile
diff --git a/biology/molden/files/patch-src_surf_utils.c b/biology/molden/files/patch-src_surf_utils.c
new file mode 100644
index 000000000000..bc05318375f8
--- /dev/null
+++ b/biology/molden/files/patch-src_surf_utils.c
@@ -0,0 +1,21 @@
+- fix return statements in the function the returns int
+
+--- src/surf/utils.c.orig	2022-07-15 23:20:39 UTC
++++ src/surf/utils.c
+@@ -91,7 +91,7 @@ float			radius;
+   disc = radius*radius - DOTPROD3(EO, EO);
+   if (FP_EQ_EPS(disc, 0, GP_EPS*GP_EPS))
+   { VEC3_ASN_OP(int_point, =, ray_pt);
+-    return;
++    return -1;
+   }
+ 
+   one_by_sq_dir_mag = 1.0/DOTPROD3(ray_dir, ray_dir);
+@@ -107,6 +107,7 @@ float			radius;
+   { t = v*one_by_sq_dir_mag - sqrt(disc*one_by_sq_dir_mag);
+     VEC3_V_OP_V_OP_S(int_point, ray_pt, +, ray_dir, *, t);
+   }
++  return -1;
+ }
+ 
+ /*----------------------------------------------------------------------------------
diff --git a/biology/molden/files/patch-src_xwin.c b/biology/molden/files/patch-src_xwin.c
new file mode 100644
index 000000000000..b16dab11bff8
--- /dev/null
+++ b/biology/molden/files/patch-src_xwin.c
@@ -0,0 +1,10 @@
+- disable GLIBC symbols specific to linux
+
+--- src/xwin.c.orig	2022-07-15 23:09:11 UTC
++++ src/xwin.c
+@@ -1,4 +1,4 @@
+-#ifndef DARWIN
++#if !defined(DARWIN) && !defined(__FreeBSD__)
+ __asm__(".symver memcpy,memcpy@GLIBC_2.2.5");
+ __asm__(".symver memmove,memmove@GLIBC_2.2.5");
+ __asm__(".symver log,log@GLIBC_2.2.5");
diff --git a/biology/molden/pkg-descr b/biology/molden/pkg-descr
index 45612201a3c7..2b20fa8c9f98 100644
--- a/biology/molden/pkg-descr
+++ b/biology/molden/pkg-descr
@@ -21,4 +21,4 @@ optimisation jobs. Molden has a powerful Z-matrix editor which give full control
 over the geometry and allows you to build molecules from scratch, including
 polypeptides.
 
-WWW: http://cheminf.cmbi.ru.nl/molden/
+WWW: https://www.theochem.ru.nl/molden/