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Message-Id: <20120926022101.4f361da137bfaa9c09ef63b8@yahoo.com>
Date: Wed, 26 Sep 2012 02:21:01 +0900
From: KATO Tsuguru <tkato432@yahoo.com>
To: FreeBSD-gnats-submit@FreeBSD.org
Subject: biology/molden: Update to version 6.0

>Number:         171970
>Category:       ports
>Synopsis:       biology/molden: Update to version 6.0
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    sperber
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Tue Sep 25 18:10:12 UTC 2012
>Closed-Date:    Sat Dec 01 08:54:27 UTC 2012
>Last-Modified:  Sat Dec 01 08:54:27 UTC 2012
>Originator:     KATO Tsuguru
>Release:        FreeBSD 7.4-RELEASE-p10 i386
>Organization:
>Environment:
>Description:
- Update to version 6.0

Remove file:
files/patch-aa
files/patch-xwin.c
pkg-plist

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/molden/Makefile biology/molden/Makefile
--- /usr/ports/biology/molden/Makefile	2012-09-24 00:40:58.000000000 +0900
+++ biology/molden/Makefile	2012-09-24 03:07:41.000000000 +0900
@@ -2,8 +2,7 @@
 # $FreeBSD: ports/biology/molden/Makefile,v 1.49 2012/09/23 15:40:58 danfe Exp $
 
 PORTNAME=	molden
-PORTVERSION=	4.6
-PORTREVISION=	3
+PORTVERSION=	5.0
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/
@@ -12,16 +11,33 @@
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Display molecular orbitals and electron densities in 2D and 3D
 
-USE_XORG=	x11 xmu
-USE_GL=		glut
-USE_FORTRAN=	yes
+RESTRICTED=	free for academic, non profit usage; do not re-distribute source and executable.
 
-RESTRICTED=	free for academic, non profit usage; do not re-distribute source and executable
-MAKEFILE=	${WRKSRC}/makefile
+OPTIONS_DEFINE=	DATA DOCS
+OPTIONS_DEFAULT=DATA
 
-.if !defined(NOPORTDOCS)
-PORTDOCS=	docs/*
-.endif
+USE_XORG=	x11
+USE_GL=		glu
+USE_FORTRAN=	yes
+USE_GMAKE=	yes
+MAKEFILE=	makefile
+MAKE_JOBS_UNSAFE=yes
+
+CFLAGS+=	-D${OPSYS:U} -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
+
+PORTDOCS=	*
+PORTDATA=	*
+PLIST_FILES=	bin/ambfor bin/gmolden bin/molden bin/surf
+
+.include <bsd.port.options.mk>
+
+post-patch:
+	@${REINPLACE_CMD} -e \
+		's|^CC |#CC | ; \
+		 s|^FC |#FC | ; \
+		 s|/usr/X11R6|${LOCALBASE}| ; \
+		 s|-lXmu|| ; \
+		 /depend/s|^|#|' ${WRKSRC}/makefile
 
 post-configure:
 	@${ECHO_MSG} "********************"
@@ -32,17 +48,18 @@
 
 do-install:
 	${INSTALL_PROGRAM} ${WRKSRC}/molden ${PREFIX}/bin
-	${INSTALL_PROGRAM} ${WRKSRC}/ambfor/ambfor ${PREFIX}/bin
 	${INSTALL_PROGRAM} ${WRKSRC}/gmolden ${PREFIX}/bin
+	${INSTALL_PROGRAM} ${WRKSRC}/ambfor/ambfor ${PREFIX}/bin
 	${INSTALL_PROGRAM} ${WRKSRC}/surf/surf ${PREFIX}/bin
-.if !defined(NOPORTDOCS)
-	@${MKDIR} ${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
-.endif
-.if !defined(NOPORTDATA)
-	@${MKDIR} ${DATADIR}/test ${DATADIR}/utils
+.if ${PORT_OPTIONS:MDATA}
+	@${MKDIR} ${DATADIR}/test
 	${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test
+	@${MKDIR} ${DATADIR}/utils
 	${INSTALL_DATA} ${WRKSRC}/utils/* ${DATADIR}/utils
 .endif
+.if ${PORT_OPTIONS:MDOCS}
+	@${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
+.endif
 
 .include <bsd.port.mk>
diff -urN /usr/ports/biology/molden/distinfo biology/molden/distinfo
--- /usr/ports/biology/molden/distinfo	2011-03-19 21:29:33.000000000 +0900
+++ biology/molden/distinfo	2012-09-23 19:27:09.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (molden4.6.tar.gz) = e18583d3e3234426b06403b056aed50e98397d6733e3b635c7011725e2816380
-SIZE (molden4.6.tar.gz) = 2786093
+SHA256 (molden5.0.tar.gz) = 595717cb9268ab7529e2677185d13ec0225c7a3e8c5b82925574f10e1a5a5476
+SIZE (molden5.0.tar.gz) = 3064448
diff -urN /usr/ports/biology/molden/files/patch-aa biology/molden/files/patch-aa
--- /usr/ports/biology/molden/files/patch-aa	2009-01-06 02:27:23.000000000 +0900
+++ biology/molden/files/patch-aa	1970-01-01 09:00:00.000000000 +0900
@@ -1,59 +0,0 @@
---- makefile.orig	2008-06-24 15:44:16.000000000 +0200
-+++ makefile	2008-11-10 22:53:22.000000000 +0100
-@@ -12,9 +12,19 @@
- #
- #	Disregard compiler warnings on rdmolf.f
- #
--CC = cc
-+#CC = cc
- LIBS =  -lX11 -lm
--LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm
-+LIBSG = -L${LOCALBASE}/lib -lGLU -lGL -lXmu -lX11 -lm
-+
-+###
-+# FreeBSD
-+#CC = gcc
-+CFLAGS += -c -DDOBACK -DHASTIMER -I${LOCALBASE}/include
-+#FC = f77
-+FFLAGS += #-Wno-globals -fno-globals
-+LIBS =  -L${LOCALBASE}/lib -lX11 -lm
-+LDR = ${FC}
-+###
- 
- # Silicon Graphics
- #CFLAGS = -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
-@@ -52,11 +66,11 @@
- # with GCC4.0 or higher replace the line with:
- # 'external gfortran_iargc'
- #
--CFLAGS = -c -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
--FC = g77
--FFLAGS =
--LIBS =  -L/usr/X11R6/lib -lX11 -lm
--LDR = g77   
-+#CFLAGS = -c -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
-+#FC = g77
-+#FFLAGS =
-+#LIBS =  -L/usr/X11R6/lib -lX11 -lm
-+#LDR = g77   
- # 64 bit machines:
- #LIBS =  -L/usr/X11R6/lib64 -lX11 -lm
- #
-@@ -191,7 +205,7 @@
- # and the full opengl version of molden 'gmolden', (does not need glut)
- # (make gmolden)
- #
--LIBSOGL = -lglut -lGLU -lGL -lXmu -lX11 -lm
-+LIBSOGL = -L${LOCALBASE}/lib -lglut -lGLU -lGL -lXmu -lX11 -lm
- #
- # on linux :
- #
-@@ -227,7 +241,7 @@
- 	$(MAKE) -C ambfor
- 
- surf/surf:	surf/*.h surf/*.c
--	$(MAKE) -C surf depend
-+	#$(MAKE) -C surf depend
- 	$(MAKE) -C surf
- 
- # noxwin will not work as long as the old ocglbck calls arent in dummys
diff -urN /usr/ports/biology/molden/files/patch-ambfor-makefile biology/molden/files/patch-ambfor-makefile
--- /usr/ports/biology/molden/files/patch-ambfor-makefile	2008-11-05 06:55:39.000000000 +0900
+++ biology/molden/files/patch-ambfor-makefile	2012-09-24 02:51:30.000000000 +0900
@@ -1,17 +1,28 @@
---- ambfor/makefile.orig	2008-10-30 10:06:37.000000000 +0100
-+++ ambfor/makefile	2008-10-30 10:07:19.000000000 +0100
-@@ -14,11 +14,11 @@
+--- ambfor/makefile.orig	2011-04-29 20:40:50.000000000 +0900
++++ ambfor/makefile	2012-09-24 02:50:23.000000000 +0900
+@@ -12,12 +12,12 @@
  #
- #CC = cc
+ # 
  
--CFLAGS = -c
--FC = g77
-+CFLAGS += -DFREEBSD=1
-+#FC = g77
- FFLAGS = -c -O3 -ffast-math
+-CFLAGS = -c -g
++CFLAGS += -c
+ #FC = g77 
+-FC = gfortran
+-FFLAGS = -c -g -ffast-math -funroll-loops -O3
++#FC = gfortran
++#FFLAGS = -c -g -ffast-math -funroll-loops -O3
  LIBS =  -lm
--LDR = g77 
-+LDR = $(FC) 
+-LDR = ${FC} -g
++LDR = ${FC}
  
- OBJS = ambfor.o angle.o bond.o charge.o conn.o enegrd.o getinp.o \
- 	param.o tors.o vdwlj.o math.o optimise.o wrtout.o
+ OBJS = angle.o bond.o charge.o conn.o enegrd.o getinp.o param.o \
+ 	tors.o vdwlj.o math.o switch.o wrtout.o pbc.o 
+@@ -47,7 +47,7 @@
+ 	$(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} -c ${FFLAGS} -o ambfor.o ambfor.f
+ 
+ allocmd.o:	alloc.c
+ 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
diff -urN /usr/ports/biology/molden/files/patch-surf-makefile biology/molden/files/patch-surf-makefile
--- /usr/ports/biology/molden/files/patch-surf-makefile	2008-11-05 06:55:39.000000000 +0900
+++ biology/molden/files/patch-surf-makefile	2012-09-24 02:46:20.000000000 +0900
@@ -1,5 +1,21 @@
---- surf/Makefile.orig	2008-10-30 10:12:27.000000000 +0100
-+++ surf/Makefile	2008-10-30 10:08:43.000000000 +0100
+--- surf/Makefile.orig	2008-08-26 02:59:06.000000000 +0900
++++ surf/Makefile	2012-09-24 02:45:55.000000000 +0900
+@@ -1,12 +1,12 @@
+ # Compilation flags
+ #CC	    = cc
+-CC	    = cc
++#CC	    = cc
+ INCLUDE     = -I. 
+ #LINCLUDE    = -lcurses -ltermcap -lm
+ LINCLUDE    = -lm
+-OPT_CFLAGS  = -O2 $(FLAGS) $(INCLUDE)
++#OPT_CFLAGS  = -O2 $(FLAGS) $(INCLUDE)
+ #CFLAGS	    = -g $(FLAGS) $(INCLUDE)
+-CFLAGS	    = -O2 $(FLAGS) $(INCLUDE)
++#CFLAGS	    = -O2 $(FLAGS) $(INCLUDE)
+ 
+ # These are the user object files in the application
+ SRCS        = surf.c io.c compute.c dual.c utils.c lp.c chull.c tessel_cases.c \
 @@ -63,46 +63,120 @@
  # DO NOT DELETE THIS LINE -- make depend depends on it.
    
diff -urN /usr/ports/biology/molden/files/patch-xwin.c biology/molden/files/patch-xwin.c
--- /usr/ports/biology/molden/files/patch-xwin.c	2008-11-11 11:21:28.000000000 +0900
+++ biology/molden/files/patch-xwin.c	1970-01-01 09:00:00.000000000 +0900
@@ -1,123 +0,0 @@
---- ./xwin.c.orig	2008-11-10 12:27:25.647441620 -0500
-+++ ./xwin.c	2008-11-10 12:29:25.515496080 -0500
-@@ -22,7 +22,7 @@
- #endif
- #if defined(DARWIN) || defined(FREEBSD)
- #else
--#include <malloc.h>
-+#include <stdlib.h>
- #endif
- #endif
- 
-@@ -3360,7 +3360,7 @@
- static int *icopth;
- static int *icoptl;
- static int *icoptm;
--static int linkat = 0;
-+static int link_at = 0;
- 
- static QBOXSTRU IANZboxes[MAXAT];
- static QBOXSTRU IZboxes[MAXAT][4];
-@@ -17466,7 +17466,7 @@
- 		if (ioniom == 1) {
- 		  int ism, isl;
- 
--		  linkat = 0;
-+		  link_at = 0;
- 
- 		  /* Counting the number of Link atoms between H and lower 
- 		     levels*/
-@@ -17479,10 +17479,10 @@
- 		     if (ionij != 0) continue;
- 		     nconn = xyz.iconn[j*(MXCON+1)];
- 		     for (k=1;k<=nconn;k++) {
--		       if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
-+		       if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
- 		     }
- 		  }
--		  linkat += 20000;
-+		  link_at += 20000;
- 		  *itotc = *icopth;
- 		  *imult = *ispopth;
- 		  if (CheckChargeMult()) {
-@@ -17503,7 +17503,7 @@
- 
- 		}  else if (ioniom == 2) {
- 
--	          linkat = 0;
-+	          link_at = 0;
- 
- 		  /* Counting the number of Link atoms between H and 
- 		       lower levels*/
-@@ -17513,10 +17513,10 @@
- 			 if(ionij != 0) continue;
- 		         nconn = xyz.iconn[j*(MXCON+1)];
- 		         for (k=1;k<=nconn;k++) {
--		           if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
-+		           if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
- 		         }
- 		  }
--		  linkat += 20000;
-+		  link_at += 20000;
- 		  *itotc = *icopth;
- 		  *imult = *ispopth;
- 		  if (CheckChargeMult()) {
-@@ -17528,7 +17528,7 @@
- 	               break;
- */
- 		  }
--	          linkat = 0;
-+	          link_at = 0;
- 
- 		  /* Counting the number of Link atoms between H+M and 
- 		     lower levels*/
-@@ -17538,10 +17538,10 @@
- 			if (ionij == 2) continue;
- 			nconn = xyz.iconn[j*(MXCON+1)];
- 			for (k=1;k<=nconn;k++) {
--			   if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 == 2) linkat++;
-+			   if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 == 2) link_at++;
- 			}
- 		  }
--		  linkat += 20000;
-+		  link_at += 20000;
- 		  *itotc = *icoptm;
- 		  *imult = *ispoptm;
- 		  if (CheckChargeMult()) {
-@@ -17556,7 +17556,7 @@
- 		  icopt = *icoptl+3;
- 		  ispopt = *ispoptl-1;
- 		}
--		linkat = 0;
-+		link_at = 0;
- 		*itotc = icopt - 3;
- 		*imult = ispopt + 1;
- 		*ito = itopt[jmode] + 1;
-@@ -17808,10 +17808,10 @@
-    ionil = 0;
- 
-    if (ioniom) {
--     ionil = 3 - (linkat / 10000);
--     linkat -= (linkat / 10000) * 10000;
-+     ionil = 3 - (link_at / 10000);
-+     link_at -= (link_at / 10000) * 10000;
-    } else {
--     linkat = 0;
-+     link_at = 0;
-    }
- 
-    if (*zmptr.ihaszm) {
-@@ -17834,10 +17834,10 @@
-       }
-    }
- /*
--   fprintf(stderr,"ionil %d ne %d itotc %d linkat %d mult %d\n",
--                   ionil,ne,*itotc,linkat,*imult);
-+   fprintf(stderr,"ionil %d ne %d itotc %d link_at %d mult %d\n",
-+                   ionil,ne,*itotc,link_at,*imult);
- */
--   ne = ne - *itotc + linkat;
-+   ne = ne - *itotc + link_at;
-    if (ne % 2 == *imult % 2) return(1);
-    return(0);
- }
diff -urN /usr/ports/biology/molden/pkg-plist biology/molden/pkg-plist
--- /usr/ports/biology/molden/pkg-plist	2008-11-11 11:21:28.000000000 +0900
+++ biology/molden/pkg-plist	1970-01-01 09:00:00.000000000 +0900
@@ -1,60 +0,0 @@
-bin/ambfor
-bin/gmolden
-bin/molden
-bin/surf
-%%PORTDOCS%%%%DOCSDIR%%/manual.txt.Z
-%%PORTDOCS%%%%DOCSDIR%%/manual.ps.Z
-%%PORTDOCS%%%%DOCSDIR%%/figures.ps.Z
-%%PORTDATA%%%%DATADIR%%/test/adf.molf
-%%PORTDATA%%%%DATADIR%%/test/ambfor_amber.xyz
-%%PORTDATA%%%%DATADIR%%/test/ambfor_gaff.xyz
-%%PORTDATA%%%%DATADIR%%/test/ampac.arc
-%%PORTDATA%%%%DATADIR%%/test/ampac.test
-%%PORTDATA%%%%DATADIR%%/test/bucky.xyz
-%%PORTDATA%%%%DATADIR%%/test/chemx.test
-%%PORTDATA%%%%DATADIR%%/test/complex2.out
-%%PORTDATA%%%%DATADIR%%/test/cpeptide.gro
-%%PORTDATA%%%%DATADIR%%/test/esp.test
-%%PORTDATA%%%%DATADIR%%/test/esp.txt
-%%PORTDATA%%%%DATADIR%%/test/esp.xyz
-%%PORTDATA%%%%DATADIR%%/test/fragment
-%%PORTDATA%%%%DATADIR%%/test/gamess_uk.freq
-%%PORTDATA%%%%DATADIR%%/test/gamess_uk.input
-%%PORTDATA%%%%DATADIR%%/test/gamess_uk.test1
-%%PORTDATA%%%%DATADIR%%/test/gamess_uk.test2
-%%PORTDATA%%%%DATADIR%%/test/gamess_us.h2o_631g_opt.out
-%%PORTDATA%%%%DATADIR%%/test/gamess_us.irc
-%%PORTDATA%%%%DATADIR%%/test/gamess_us_uhf_opt
-%%PORTDATA%%%%DATADIR%%/test/gaussian.freq
-%%PORTDATA%%%%DATADIR%%/test/gaussian.input
-%%PORTDATA%%%%DATADIR%%/test/gaussian.test
-%%PORTDATA%%%%DATADIR%%/test/jaguar.cube
-%%PORTDATA%%%%DATADIR%%/test/molden.ogl
-%%PORTDATA%%%%DATADIR%%/test/mopac.freq
-%%PORTDATA%%%%DATADIR%%/test/mopac.test
-%%PORTDATA%%%%DATADIR%%/test/pdb.test
-%%PORTDATA%%%%DATADIR%%/test/pdb.test.omap
-%%PORTDATA%%%%DATADIR%%/test/qchem.test
-%%PORTDATA%%%%DATADIR%%/test/reacpth.xyz
-%%PORTDATA%%%%DATADIR%%/test/shelx.ins
-%%PORTDATA%%%%DATADIR%%/test/surface.molf
-%%PORTDATA%%%%DATADIR%%/test/test.fdat
-%%PORTDATA%%%%DATADIR%%/test/test.mol2
-%%PORTDATA%%%%DATADIR%%/test/test_homo.cube
-%%PORTDATA%%%%DATADIR%%/test/tinker_charmm.xyz
-%%PORTDATA%%%%DATADIR%%/test/tinker_mm3.xyz
-%%PORTDATA%%%%DATADIR%%/test/uracil.fdat
-%%PORTDATA%%%%DATADIR%%/test/uracil_gauss.out
-%%PORTDATA%%%%DATADIR%%/test/vamp.test
-%%PORTDATA%%%%DATADIR%%/utils/INFO
-%%PORTDATA%%%%DATADIR%%/utils/ch_backspace
-%%PORTDATA%%%%DATADIR%%/utils/ch_mxcon
-%%PORTDATA%%%%DATADIR%%/utils/ch_par
-%%PORTDATA%%%%DATADIR%%/utils/colors
-%%PORTDATA%%%%DATADIR%%/utils/ircextract.awk
-%%PORTDATA%%%%DATADIR%%/utils/molden
-%%PORTDATA%%%%DATADIR%%/utils/multi_vrml.csh
-%%PORTDATA%%%%DATADIR%%/utils/multi_vrml_orbitals.csh
-%%PORTDATA%%@dirrm %%DATADIR%%/utils
-%%PORTDATA%%@dirrm %%DATADIR%%/test
-%%PORTDATA%%@dirrm %%DATADIR%%
>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->miwi 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Tue Sep 25 18:11:41 UTC 2012 
Responsible-Changed-Why:  
miwi@ wants his PRs (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=171970 

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/171970: biology/molden: Update to version 6.0
Date: Mon, 1 Oct 2012 02:59:21 +0900

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 Version 5.0.2 has been relesed.
 
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 diff -urN /usr/ports/biology/molden/Makefile biology/molden/Makefile
 --- /usr/ports/biology/molden/Makefile	2012-09-24 00:40:58.000000000 +0900
 +++ biology/molden/Makefile	2012-10-01 02:46:12.000000000 +0900
 @@ -2,8 +2,7 @@
  # $FreeBSD: ports/biology/molden/Makefile,v 1.49 2012/09/23 15:40:58 danfe Exp $
  
  PORTNAME=	molden
 -PORTVERSION=	4.6
 -PORTREVISION=	3
 +PORTVERSION=	5.0.2
  PORTEPOCH=	1
  CATEGORIES=	biology
  MASTER_SITES=	ftp://ftp.cmbi.ru.nl/pub/molgraph/molden/
 @@ -12,16 +11,35 @@
  MAINTAINER=	ports@FreeBSD.org
  COMMENT=	Display molecular orbitals and electron densities in 2D and 3D
  
 -USE_XORG=	x11 xmu
 -USE_GL=		glut
 -USE_FORTRAN=	yes
 +RESTRICTED=	free for academic, non profit usage; do not re-distribute source and executable.
  
 -RESTRICTED=	free for academic, non profit usage; do not re-distribute source and executable
 -MAKEFILE=	${WRKSRC}/makefile
 +OPTIONS_DEFINE=	DATA DOCS
 +OPTIONS_DEFAULT=DATA
  
 -.if !defined(NOPORTDOCS)
 -PORTDOCS=	docs/*
 -.endif
 +WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION:R}
 +
 +USE_XORG=	x11
 +USE_GL=		glu
 +USE_FORTRAN=	yes
 +USE_GMAKE=	yes
 +MAKEFILE=	makefile
 +MAKE_JOBS_UNSAFE=yes
 +
 +CFLAGS+=	-D${OPSYS:U} -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
 +
 +PORTDOCS=	*
 +PORTDATA=	*
 +PLIST_FILES=	bin/ambfor bin/gmolden bin/molden bin/surf
 +
 +.include <bsd.port.options.mk>
 +
 +post-patch:
 +	@${REINPLACE_CMD} -e \
 +		's|^CC |#CC | ; \
 +		 s|^FC |#FC | ; \
 +		 s|/usr/X11R6|${LOCALBASE}| ; \
 +		 s|-lXmu|| ; \
 +		 /depend/s|^|#|' ${WRKSRC}/makefile
  
  post-configure:
  	@${ECHO_MSG} "********************"
 @@ -32,17 +50,18 @@
  
  do-install:
  	${INSTALL_PROGRAM} ${WRKSRC}/molden ${PREFIX}/bin
 -	${INSTALL_PROGRAM} ${WRKSRC}/ambfor/ambfor ${PREFIX}/bin
  	${INSTALL_PROGRAM} ${WRKSRC}/gmolden ${PREFIX}/bin
 +	${INSTALL_PROGRAM} ${WRKSRC}/ambfor/ambfor ${PREFIX}/bin
  	${INSTALL_PROGRAM} ${WRKSRC}/surf/surf ${PREFIX}/bin
 -.if !defined(NOPORTDOCS)
 -	@${MKDIR} ${DOCSDIR}
 -	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
 -.endif
 -.if !defined(NOPORTDATA)
 -	@${MKDIR} ${DATADIR}/test ${DATADIR}/utils
 +.if ${PORT_OPTIONS:MDATA}
 +	@${MKDIR} ${DATADIR}/test
  	${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test
 +	@${MKDIR} ${DATADIR}/utils
  	${INSTALL_DATA} ${WRKSRC}/utils/* ${DATADIR}/utils
  .endif
 +.if ${PORT_OPTIONS:MDOCS}
 +	@${MKDIR} ${DOCSDIR}
 +	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
 +.endif
  
  .include <bsd.port.mk>
 diff -urN /usr/ports/biology/molden/distinfo biology/molden/distinfo
 --- /usr/ports/biology/molden/distinfo	2011-03-19 21:29:33.000000000 +0900
 +++ biology/molden/distinfo	2012-10-01 02:45:30.000000000 +0900
 @@ -1,2 +1,2 @@
 -SHA256 (molden4.6.tar.gz) = e18583d3e3234426b06403b056aed50e98397d6733e3b635c7011725e2816380
 -SIZE (molden4.6.tar.gz) = 2786093
 +SHA256 (molden5.0.2.tar.gz) = cfe48142fa7f59dfb5f90d63e26ae3d7d29b5ab02c0f9424bceef9f7d27f0709
 +SIZE (molden5.0.2.tar.gz) = 3064536
 diff -urN /usr/ports/biology/molden/files/patch-aa biology/molden/files/patch-aa
 --- /usr/ports/biology/molden/files/patch-aa	2009-01-06 02:27:23.000000000 +0900
 +++ biology/molden/files/patch-aa	1970-01-01 09:00:00.000000000 +0900
 @@ -1,59 +0,0 @@
 ---- makefile.orig	2008-06-24 15:44:16.000000000 +0200
 -+++ makefile	2008-11-10 22:53:22.000000000 +0100
 -@@ -12,9 +12,19 @@
 - #
 - #	Disregard compiler warnings on rdmolf.f
 - #
 --CC = cc
 -+#CC = cc
 - LIBS =  -lX11 -lm
 --LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm
 -+LIBSG = -L${LOCALBASE}/lib -lGLU -lGL -lXmu -lX11 -lm
 -+
 -+###
 -+# FreeBSD
 -+#CC = gcc
 -+CFLAGS += -c -DDOBACK -DHASTIMER -I${LOCALBASE}/include
 -+#FC = f77
 -+FFLAGS += #-Wno-globals -fno-globals
 -+LIBS =  -L${LOCALBASE}/lib -lX11 -lm
 -+LDR = ${FC}
 -+###
 - 
 - # Silicon Graphics
 - #CFLAGS = -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
 -@@ -52,11 +66,11 @@
 - # with GCC4.0 or higher replace the line with:
 - # 'external gfortran_iargc'
 - #
 --CFLAGS = -c -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
 --FC = g77
 --FFLAGS =
 --LIBS =  -L/usr/X11R6/lib -lX11 -lm
 --LDR = g77   
 -+#CFLAGS = -c -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0
 -+#FC = g77
 -+#FFLAGS =
 -+#LIBS =  -L/usr/X11R6/lib -lX11 -lm
 -+#LDR = g77   
 - # 64 bit machines:
 - #LIBS =  -L/usr/X11R6/lib64 -lX11 -lm
 - #
 -@@ -191,7 +205,7 @@
 - # and the full opengl version of molden 'gmolden', (does not need glut)
 - # (make gmolden)
 - #
 --LIBSOGL = -lglut -lGLU -lGL -lXmu -lX11 -lm
 -+LIBSOGL = -L${LOCALBASE}/lib -lglut -lGLU -lGL -lXmu -lX11 -lm
 - #
 - # on linux :
 - #
 -@@ -227,7 +241,7 @@
 - 	$(MAKE) -C ambfor
 - 
 - surf/surf:	surf/*.h surf/*.c
 --	$(MAKE) -C surf depend
 -+	#$(MAKE) -C surf depend
 - 	$(MAKE) -C surf
 - 
 - # noxwin will not work as long as the old ocglbck calls arent in dummys
 diff -urN /usr/ports/biology/molden/files/patch-ambfor-makefile biology/molden/files/patch-ambfor-makefile
 --- /usr/ports/biology/molden/files/patch-ambfor-makefile	2008-11-05 06:55:39.000000000 +0900
 +++ biology/molden/files/patch-ambfor-makefile	2012-09-24 02:51:30.000000000 +0900
 @@ -1,17 +1,28 @@
 ---- ambfor/makefile.orig	2008-10-30 10:06:37.000000000 +0100
 -+++ ambfor/makefile	2008-10-30 10:07:19.000000000 +0100
 -@@ -14,11 +14,11 @@
 +--- ambfor/makefile.orig	2011-04-29 20:40:50.000000000 +0900
 ++++ ambfor/makefile	2012-09-24 02:50:23.000000000 +0900
 +@@ -12,12 +12,12 @@
   #
 - #CC = cc
 + # 
   
 --CFLAGS = -c
 --FC = g77
 -+CFLAGS += -DFREEBSD=1
 -+#FC = g77
 - FFLAGS = -c -O3 -ffast-math
 +-CFLAGS = -c -g
 ++CFLAGS += -c
 + #FC = g77 
 +-FC = gfortran
 +-FFLAGS = -c -g -ffast-math -funroll-loops -O3
 ++#FC = gfortran
 ++#FFLAGS = -c -g -ffast-math -funroll-loops -O3
   LIBS =  -lm
 --LDR = g77 
 -+LDR = $(FC) 
 +-LDR = ${FC} -g
 ++LDR = ${FC}
   
 - OBJS = ambfor.o angle.o bond.o charge.o conn.o enegrd.o getinp.o \
 - 	param.o tors.o vdwlj.o math.o optimise.o wrtout.o
 + OBJS = angle.o bond.o charge.o conn.o enegrd.o getinp.o param.o \
 + 	tors.o vdwlj.o math.o switch.o wrtout.o pbc.o 
 +@@ -47,7 +47,7 @@
 + 	$(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} -c ${FFLAGS} -o ambfor.o ambfor.f
 + 
 + allocmd.o:	alloc.c
 + 	$(CC) $(CFLAGS) -DMD -c alloc.c -o allocmd.o
 diff -urN /usr/ports/biology/molden/files/patch-surf-makefile biology/molden/files/patch-surf-makefile
 --- /usr/ports/biology/molden/files/patch-surf-makefile	2008-11-05 06:55:39.000000000 +0900
 +++ biology/molden/files/patch-surf-makefile	2012-09-24 02:46:20.000000000 +0900
 @@ -1,5 +1,21 @@
 ---- surf/Makefile.orig	2008-10-30 10:12:27.000000000 +0100
 -+++ surf/Makefile	2008-10-30 10:08:43.000000000 +0100
 +--- surf/Makefile.orig	2008-08-26 02:59:06.000000000 +0900
 ++++ surf/Makefile	2012-09-24 02:45:55.000000000 +0900
 +@@ -1,12 +1,12 @@
 + # Compilation flags
 + #CC	    = cc
 +-CC	    = cc
 ++#CC	    = cc
 + INCLUDE     = -I. 
 + #LINCLUDE    = -lcurses -ltermcap -lm
 + LINCLUDE    = -lm
 +-OPT_CFLAGS  = -O2 $(FLAGS) $(INCLUDE)
 ++#OPT_CFLAGS  = -O2 $(FLAGS) $(INCLUDE)
 + #CFLAGS	    = -g $(FLAGS) $(INCLUDE)
 +-CFLAGS	    = -O2 $(FLAGS) $(INCLUDE)
 ++#CFLAGS	    = -O2 $(FLAGS) $(INCLUDE)
 + 
 + # These are the user object files in the application
 + SRCS        = surf.c io.c compute.c dual.c utils.c lp.c chull.c tessel_cases.c \
  @@ -63,46 +63,120 @@
   # DO NOT DELETE THIS LINE -- make depend depends on it.
     
 diff -urN /usr/ports/biology/molden/files/patch-xwin.c biology/molden/files/patch-xwin.c
 --- /usr/ports/biology/molden/files/patch-xwin.c	2008-11-11 11:21:28.000000000 +0900
 +++ biology/molden/files/patch-xwin.c	1970-01-01 09:00:00.000000000 +0900
 @@ -1,123 +0,0 @@
 ---- ./xwin.c.orig	2008-11-10 12:27:25.647441620 -0500
 -+++ ./xwin.c	2008-11-10 12:29:25.515496080 -0500
 -@@ -22,7 +22,7 @@
 - #endif
 - #if defined(DARWIN) || defined(FREEBSD)
 - #else
 --#include <malloc.h>
 -+#include <stdlib.h>
 - #endif
 - #endif
 - 
 -@@ -3360,7 +3360,7 @@
 - static int *icopth;
 - static int *icoptl;
 - static int *icoptm;
 --static int linkat = 0;
 -+static int link_at = 0;
 - 
 - static QBOXSTRU IANZboxes[MAXAT];
 - static QBOXSTRU IZboxes[MAXAT][4];
 -@@ -17466,7 +17466,7 @@
 - 		if (ioniom == 1) {
 - 		  int ism, isl;
 - 
 --		  linkat = 0;
 -+		  link_at = 0;
 - 
 - 		  /* Counting the number of Link atoms between H and lower 
 - 		     levels*/
 -@@ -17479,10 +17479,10 @@
 - 		     if (ionij != 0) continue;
 - 		     nconn = xyz.iconn[j*(MXCON+1)];
 - 		     for (k=1;k<=nconn;k++) {
 --		       if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
 -+		       if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
 - 		     }
 - 		  }
 --		  linkat += 20000;
 -+		  link_at += 20000;
 - 		  *itotc = *icopth;
 - 		  *imult = *ispopth;
 - 		  if (CheckChargeMult()) {
 -@@ -17503,7 +17503,7 @@
 - 
 - 		}  else if (ioniom == 2) {
 - 
 --	          linkat = 0;
 -+	          link_at = 0;
 - 
 - 		  /* Counting the number of Link atoms between H and 
 - 		       lower levels*/
 -@@ -17513,10 +17513,10 @@
 - 			 if(ionij != 0) continue;
 - 		         nconn = xyz.iconn[j*(MXCON+1)];
 - 		         for (k=1;k<=nconn;k++) {
 --		           if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
 -+		           if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
 - 		         }
 - 		  }
 --		  linkat += 20000;
 -+		  link_at += 20000;
 - 		  *itotc = *icopth;
 - 		  *imult = *ispopth;
 - 		  if (CheckChargeMult()) {
 -@@ -17528,7 +17528,7 @@
 - 	               break;
 - */
 - 		  }
 --	          linkat = 0;
 -+	          link_at = 0;
 - 
 - 		  /* Counting the number of Link atoms between H+M and 
 - 		     lower levels*/
 -@@ -17538,10 +17538,10 @@
 - 			if (ionij == 2) continue;
 - 			nconn = xyz.iconn[j*(MXCON+1)];
 - 			for (k=1;k<=nconn;k++) {
 --			   if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 == 2) linkat++;
 -+			   if (xyz.ityp[xyz.iconn[j*(MXCON+1)+k]-1]/10000 == 2) link_at++;
 - 			}
 - 		  }
 --		  linkat += 20000;
 -+		  link_at += 20000;
 - 		  *itotc = *icoptm;
 - 		  *imult = *ispoptm;
 - 		  if (CheckChargeMult()) {
 -@@ -17556,7 +17556,7 @@
 - 		  icopt = *icoptl+3;
 - 		  ispopt = *ispoptl-1;
 - 		}
 --		linkat = 0;
 -+		link_at = 0;
 - 		*itotc = icopt - 3;
 - 		*imult = ispopt + 1;
 - 		*ito = itopt[jmode] + 1;
 -@@ -17808,10 +17808,10 @@
 -    ionil = 0;
 - 
 -    if (ioniom) {
 --     ionil = 3 - (linkat / 10000);
 --     linkat -= (linkat / 10000) * 10000;
 -+     ionil = 3 - (link_at / 10000);
 -+     link_at -= (link_at / 10000) * 10000;
 -    } else {
 --     linkat = 0;
 -+     link_at = 0;
 -    }
 - 
 -    if (*zmptr.ihaszm) {
 -@@ -17834,10 +17834,10 @@
 -       }
 -    }
 - /*
 --   fprintf(stderr,"ionil %d ne %d itotc %d linkat %d mult %d\n",
 --                   ionil,ne,*itotc,linkat,*imult);
 -+   fprintf(stderr,"ionil %d ne %d itotc %d link_at %d mult %d\n",
 -+                   ionil,ne,*itotc,link_at,*imult);
 - */
 --   ne = ne - *itotc + linkat;
 -+   ne = ne - *itotc + link_at;
 -    if (ne % 2 == *imult % 2) return(1);
 -    return(0);
 - }
 diff -urN /usr/ports/biology/molden/pkg-plist biology/molden/pkg-plist
 --- /usr/ports/biology/molden/pkg-plist	2008-11-11 11:21:28.000000000 +0900
 +++ biology/molden/pkg-plist	1970-01-01 09:00:00.000000000 +0900
 @@ -1,60 +0,0 @@
 -bin/ambfor
 -bin/gmolden
 -bin/molden
 -bin/surf
 -%%PORTDOCS%%%%DOCSDIR%%/manual.txt.Z
 -%%PORTDOCS%%%%DOCSDIR%%/manual.ps.Z
 -%%PORTDOCS%%%%DOCSDIR%%/figures.ps.Z
 -%%PORTDATA%%%%DATADIR%%/test/adf.molf
 -%%PORTDATA%%%%DATADIR%%/test/ambfor_amber.xyz
 -%%PORTDATA%%%%DATADIR%%/test/ambfor_gaff.xyz
 -%%PORTDATA%%%%DATADIR%%/test/ampac.arc
 -%%PORTDATA%%%%DATADIR%%/test/ampac.test
 -%%PORTDATA%%%%DATADIR%%/test/bucky.xyz
 -%%PORTDATA%%%%DATADIR%%/test/chemx.test
 -%%PORTDATA%%%%DATADIR%%/test/complex2.out
 -%%PORTDATA%%%%DATADIR%%/test/cpeptide.gro
 -%%PORTDATA%%%%DATADIR%%/test/esp.test
 -%%PORTDATA%%%%DATADIR%%/test/esp.txt
 -%%PORTDATA%%%%DATADIR%%/test/esp.xyz
 -%%PORTDATA%%%%DATADIR%%/test/fragment
 -%%PORTDATA%%%%DATADIR%%/test/gamess_uk.freq
 -%%PORTDATA%%%%DATADIR%%/test/gamess_uk.input
 -%%PORTDATA%%%%DATADIR%%/test/gamess_uk.test1
 -%%PORTDATA%%%%DATADIR%%/test/gamess_uk.test2
 -%%PORTDATA%%%%DATADIR%%/test/gamess_us.h2o_631g_opt.out
 -%%PORTDATA%%%%DATADIR%%/test/gamess_us.irc
 -%%PORTDATA%%%%DATADIR%%/test/gamess_us_uhf_opt
 -%%PORTDATA%%%%DATADIR%%/test/gaussian.freq
 -%%PORTDATA%%%%DATADIR%%/test/gaussian.input
 -%%PORTDATA%%%%DATADIR%%/test/gaussian.test
 -%%PORTDATA%%%%DATADIR%%/test/jaguar.cube
 -%%PORTDATA%%%%DATADIR%%/test/molden.ogl
 -%%PORTDATA%%%%DATADIR%%/test/mopac.freq
 -%%PORTDATA%%%%DATADIR%%/test/mopac.test
 -%%PORTDATA%%%%DATADIR%%/test/pdb.test
 -%%PORTDATA%%%%DATADIR%%/test/pdb.test.omap
 -%%PORTDATA%%%%DATADIR%%/test/qchem.test
 -%%PORTDATA%%%%DATADIR%%/test/reacpth.xyz
 -%%PORTDATA%%%%DATADIR%%/test/shelx.ins
 -%%PORTDATA%%%%DATADIR%%/test/surface.molf
 -%%PORTDATA%%%%DATADIR%%/test/test.fdat
 -%%PORTDATA%%%%DATADIR%%/test/test.mol2
 -%%PORTDATA%%%%DATADIR%%/test/test_homo.cube
 -%%PORTDATA%%%%DATADIR%%/test/tinker_charmm.xyz
 -%%PORTDATA%%%%DATADIR%%/test/tinker_mm3.xyz
 -%%PORTDATA%%%%DATADIR%%/test/uracil.fdat
 -%%PORTDATA%%%%DATADIR%%/test/uracil_gauss.out
 -%%PORTDATA%%%%DATADIR%%/test/vamp.test
 -%%PORTDATA%%%%DATADIR%%/utils/INFO
 -%%PORTDATA%%%%DATADIR%%/utils/ch_backspace
 -%%PORTDATA%%%%DATADIR%%/utils/ch_mxcon
 -%%PORTDATA%%%%DATADIR%%/utils/ch_par
 -%%PORTDATA%%%%DATADIR%%/utils/colors
 -%%PORTDATA%%%%DATADIR%%/utils/ircextract.awk
 -%%PORTDATA%%%%DATADIR%%/utils/molden
 -%%PORTDATA%%%%DATADIR%%/utils/multi_vrml.csh
 -%%PORTDATA%%%%DATADIR%%/utils/multi_vrml_orbitals.csh
 -%%PORTDATA%%@dirrm %%DATADIR%%/utils
 -%%PORTDATA%%@dirrm %%DATADIR%%/test
 -%%PORTDATA%%@dirrm %%DATADIR%%
 
 --Multipart=_Mon__1_Oct_2012_02_59_21_+0900_jYG+wHJbMDKFIA6x--
Responsible-Changed-From-To: miwi->freebsd-ports-bugs 
Responsible-Changed-By: bapt 
Responsible-Changed-When: Mon Oct 29 09:51:28 UTC 2012 
Responsible-Changed-Why:  
Reassign to the heap miwi being overloaded for now 

http://www.freebsd.org/cgi/query-pr.cgi?pr=171970 
Responsible-Changed-From-To: freebsd-ports-bugs->sperber 
Responsible-Changed-By: sperber 
Responsible-Changed-When: Mon Oct 29 17:55:55 UTC 2012 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=171970 
State-Changed-From-To: open->closed 
State-Changed-By: sperber 
State-Changed-When: Sat Dec 1 08:54:26 UTC 2012 
State-Changed-Why:  
Committed. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=171970 
>Unformatted:
