git: 42231a31fd41 - main - biology/molden: update 7.1 → 7.3

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Thu, 10 Sep 2026 20:07:00 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=42231a31fd41f0c1f53eef2eb856f8f44a285d1e

commit 42231a31fd41f0c1f53eef2eb856f8f44a285d1e
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-09-10 19:12:10 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-09-10 20:04:57 +0000

    biology/molden: update 7.1 → 7.3
---
 biology/molden/Makefile                      |  5 ++--
 biology/molden/distinfo                      |  6 ++--
 biology/molden/files/patch-makefile          | 41 ++--------------------------
 biology/molden/files/patch-src_surf_Makefile | 13 ---------
 biology/molden/files/patch-src_surf_utils.c  | 21 --------------
 biology/molden/files/patch-src_xwin.c        | 10 -------
 6 files changed, 9 insertions(+), 87 deletions(-)

diff --git a/biology/molden/Makefile b/biology/molden/Makefile
index eca344515e3c..14ded9d01ddd 100644
--- a/biology/molden/Makefile
+++ b/biology/molden/Makefile
@@ -1,6 +1,5 @@
 PORTNAME=	molden
-DISTVERSION=	7.1
-PORTREVISION=	1
+DISTVERSION=	7.3
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	https://ftp.science.ru.nl/Molden/
@@ -35,6 +34,8 @@ PLIST_FILES=	bin/ambfor \
 		bin/molden \
 		bin/surf
 
+BINARY_ALIAS=	gcc=${CC}
+
 PORTSCOUT=	limit:^5\.0\.
 
 OPTIONS_DEFINE=		DATA DOCS
diff --git a/biology/molden/distinfo b/biology/molden/distinfo
index c661feebb345..814cdcdf0e44 100644
--- a/biology/molden/distinfo
+++ b/biology/molden/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1657929531
-SHA256 (molden7.1.tar.gz) = 98a39f0aa1667c14c36f40c0251522984245e5ba282af8fbc8a2f06079e40d43
-SIZE (molden7.1.tar.gz) = 14645590
+TIMESTAMP = 1789067028
+SHA256 (molden7.3.tar.gz) = 870f4fa6635229791bb09bbbd07f51456b2c90101d73564dc47ed7769b8c07a1
+SIZE (molden7.3.tar.gz) = 7151194
diff --git a/biology/molden/files/patch-makefile b/biology/molden/files/patch-makefile
index b5cba7470955..a339b08fc463 100644
--- a/biology/molden/files/patch-makefile
+++ b/biology/molden/files/patch-makefile
@@ -1,43 +1,8 @@
 - pass supplied FFLAGS to the build
 
---- makefile.orig	2022-01-21 11:28:48 UTC
+--- makefile.orig	2023-05-24 07:18:35 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
-@@ -132,12 +132,12 @@ 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 -fallow-argument-mismatch
-+FFLAGS+=-O3 -funroll-loops -fallow-argument-mismatch
- 
- 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-tautological-pointer-compare -Wno-tautological-constant-out-of-range-compare -fallow-argument-mismatch
-@@ -307,16 +307,16 @@ 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
+@@ -312,7 +312,7 @@ surf/surf:	src/surf/*.h src/surf/*.c
  
  surf/surf:	src/surf/*.h src/surf/*.c
  	$(MAKE) -C src/surf depend 
@@ -45,4 +10,4 @@
 +	$(MAKE) -C src/surf EXT="${EXT}" FFLAGS="$(FFLAGS)"
  	mv src/surf/surf bin/surf
  
- # noxwin will not work as long as the old ocglbck calls arent in dummys
+ docker/docker:	docker/*.f docker/*.c
diff --git a/biology/molden/files/patch-src_surf_Makefile b/biology/molden/files/patch-src_surf_Makefile
deleted file mode 100644
index ca1673d9c3cf..000000000000
--- a/biology/molden/files/patch-src_surf_Makefile
+++ /dev/null
@@ -1,13 +0,0 @@
-- 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
deleted file mode 100644
index bc05318375f8..000000000000
--- a/biology/molden/files/patch-src_surf_utils.c
+++ /dev/null
@@ -1,21 +0,0 @@
-- 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
deleted file mode 100644
index b16dab11bff8..000000000000
--- a/biology/molden/files/patch-src_xwin.c
+++ /dev/null
@@ -1,10 +0,0 @@
-- 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");