5 files changed, 117 insertions, 110 deletions

diff --git a/biology/molden/Makefile b/biology/molden/Makefile
index 177b352b4c09..a16f75d51f32 100644
--- a/biology/molden/Makefile
+++ b/biology/molden/Makefile
@@ -6,7 +6,8 @@
 #
 
 PORTNAME=	molden
-PORTVERSION=	4.7
+PORTVERSION=	4.6
+PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.cmbi.kun.nl/pub/molgraph/molden/
 DISTNAME=	${PORTNAME}${PORTVERSION}
@@ -15,8 +16,6 @@ DIST_SUBDIR=	${PKGNAME}
 MAINTAINER=	oivulf@gmail.com
 COMMENT=	Display molecular orbitals and electron densities in 2D and 3D
 
-BROKEN=		Does not fetch
-
 USE_XORG=	x11 xmu
 USE_GL=		glut
 USE_FORTRAN=	yes
@@ -28,9 +27,6 @@ MAKEFILE=	${WRKSRC}/makefile
 PORTDOCS=	docs/*
 .endif
 
-post-patch:
-	@${REINPLACE_CMD} -e 's,malloc.h,stdlib.h,' ${WRKSRC}/xwin.c
-
 post-configure:
 	@${ECHO_MSG} "********************"
 	@${ECHO_MSG} "**  If you want to use a larger MOLDEN,"
@@ -47,9 +43,11 @@ do-install:
 	${MKDIR} ${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
 .endif
-	${MKDIR} ${PREFIX}/share/molden/test
-	${MKDIR} ${PREFIX}/share/molden/utils
-	${INSTALL_DATA} ${WRKSRC}/test/* ${PREFIX}/share/molden/test
-	${INSTALL_DATA} ${WRKSRC}/utils/* ${PREFIX}/share/molden/utils
+.if !defined(NOPORTDATA)
+	${MKDIR} ${DATADIR}/test
+	${MKDIR} ${DATADIR}/utils
+	${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test
+	${INSTALL_DATA} ${WRKSRC}/utils/* ${DATADIR}/utils
+.endif
 
 .include <bsd.port.mk>
diff --git a/biology/molden/distinfo b/biology/molden/distinfo
index 9fbacbc7a84f..ad263a13e821 100644
--- a/biology/molden/distinfo
+++ b/biology/molden/distinfo
@@ -1,3 +1,3 @@
-MD5 (molden-4.7/molden4.7.tar.gz) = 27ed92f0e4a7e7ff02879f72f06e4af8
-SHA256 (molden-4.7/molden4.7.tar.gz) = d76facb939f912f493b480669f39474a2b848dbbd3d5515835ca0fbc57cdad37
-SIZE (molden-4.7/molden4.7.tar.gz) = 2817858
+MD5 (molden-4.6,1/molden4.6.tar.gz) = 3b4e7fa4a323c7e283c0348fc6bb3b2d
+SHA256 (molden-4.6,1/molden4.6.tar.gz) = e18583d3e3234426b06403b056aed50e98397d6733e3b635c7011725e2816380
+SIZE (molden-4.6,1/molden4.6.tar.gz) = 2786093
diff --git a/biology/molden/files/patch-makefile b/biology/molden/files/patch-aa
index ac9cc36e67b1..e4c75e6ed719 100644
--- a/biology/molden/files/patch-makefile
+++ b/biology/molden/files/patch-aa
@@ -1,5 +1,5 @@
---- makefile.orig	2008-08-25 19:55:57.000000000 +0200
-+++ makefile	2008-11-01 21:48:37.000000000 +0100
+--- makefile.orig	2008-06-24 15:44:16.000000000 +0200
++++ makefile	2008-11-10 22:53:22.000000000 +0100
 @@ -12,9 +12,23 @@
  #
  #	Disregard compiler warnings on rdmolf.f
@@ -57,7 +57,7 @@
  
  surf/surf:	surf/*.h surf/*.c
 -	$(MAKE) -C surf depend
-+#	$(MAKE) -C surf depend
++	#$(MAKE) -C surf depend
  	$(MAKE) -C surf
  
  # noxwin will not work as long as the old ocglbck calls arent in dummys
diff --git a/biology/molden/files/patch-xwin.c b/biology/molden/files/patch-xwin.c
index bb8017792ddf..f521bc4e51a5 100644
--- a/biology/molden/files/patch-xwin.c
+++ b/biology/molden/files/patch-xwin.c
@@ -1,15 +1,24 @@
---- xwin.c.orig	2008-11-03 09:37:45.707629185 -0500
-+++ xwin.c	2008-11-03 09:37:55.118628907 -0500
-@@ -3747,7 +3747,7 @@
- static int ibopth = 0;
- static int iboptl = 0;
- static int iboptm = 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];
-@@ -19086,7 +19086,7 @@
+@@ -17466,7 +17466,7 @@
  		if (ioniom == 1) {
  		  int ism, isl;
  
@@ -18,20 +27,20 @@
  
  		  /* Counting the number of Link atoms between H and lower 
  		     levels*/
-@@ -19099,10 +19099,10 @@
+@@ -17479,10 +17479,10 @@
  		     if (ionij != 0) continue;
- 		     nconn = xyzp->iconn[j*(MXCON+1)];
+ 		     nconn = xyz.iconn[j*(MXCON+1)];
  		     for (k=1;k<=nconn;k++) {
--		       if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
-+		       if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
+-		       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;
- 		  jobcom->itotc = jobcom->icopth;
- 		  jobcom->imult = jobcom->ispopth;
+ 		  *itotc = *icopth;
+ 		  *imult = *ispopth;
  		  if (CheckChargeMult()) {
-@@ -19123,7 +19123,7 @@
+@@ -17503,7 +17503,7 @@
  
  		}  else if (ioniom == 2) {
  
@@ -40,20 +49,20 @@
  
  		  /* Counting the number of Link atoms between H and 
  		       lower levels*/
-@@ -19133,10 +19133,10 @@
+@@ -17513,10 +17513,10 @@
  			 if(ionij != 0) continue;
- 		         nconn = xyzp->iconn[j*(MXCON+1)];
+ 		         nconn = xyz.iconn[j*(MXCON+1)];
  		         for (k=1;k<=nconn;k++) {
--		           if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) linkat++;
-+		           if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 > 0) link_at++;
+-		           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;
- 		  jobcom->itotc = jobcom->icopth;
- 		  jobcom->imult = jobcom->ispopth;
+ 		  *itotc = *icopth;
+ 		  *imult = *ispopth;
  		  if (CheckChargeMult()) {
-@@ -19148,7 +19148,7 @@
+@@ -17528,7 +17528,7 @@
  	               break;
  */
  		  }
@@ -62,29 +71,29 @@
  
  		  /* Counting the number of Link atoms between H+M and 
  		     lower levels*/
-@@ -19158,10 +19158,10 @@
+@@ -17538,10 +17538,10 @@
  			if (ionij == 2) continue;
- 			nconn = xyzp->iconn[j*(MXCON+1)];
+ 			nconn = xyz.iconn[j*(MXCON+1)];
  			for (k=1;k<=nconn;k++) {
--			   if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 == 2) linkat++;
-+			   if (xyzp->ityp[xyzp->iconn[j*(MXCON+1)+k]-1]/10000 == 2) link_at++;
+-			   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;
- 		  jobcom->itotc = jobcom->icoptm;
- 		  jobcom->imult = jobcom->ispoptm;
+ 		  *itotc = *icoptm;
+ 		  *imult = *ispoptm;
  		  if (CheckChargeMult()) {
-@@ -19176,7 +19176,7 @@
- 		  icopt = jobcom->icoptl+3;
- 		  ispopt = jobcom->ispoptl-1;
+@@ -17556,7 +17556,7 @@
+ 		  icopt = *icoptl+3;
+ 		  ispopt = *ispoptl-1;
  		}
 -		linkat = 0;
 +		link_at = 0;
- 		jobcom->itotc = icopt - 3;
- 		jobcom->imult = ispopt + 1;
- 		jobcom->ito = itopt[jmode] + 1;
-@@ -19428,10 +19428,10 @@
+ 		*itotc = icopt - 3;
+ 		*imult = ispopt + 1;
+ 		*ito = itopt[jmode] + 1;
+@@ -17808,10 +17808,10 @@
     ionil = 0;
  
     if (ioniom) {
@@ -97,18 +106,18 @@
 +     link_at = 0;
     }
  
-    if (*zmptrp->ihaszm) {
-@@ -19454,10 +19454,10 @@
+    if (*zmptr.ihaszm) {
+@@ -17834,10 +17834,10 @@
        }
     }
  /*
 -   fprintf(stderr,"ionil %d ne %d itotc %d linkat %d mult %d\n",
--                   ionil,ne,jobcom->itotc,linkat,jobcom->imult);
+-                   ionil,ne,*itotc,linkat,*imult);
 +   fprintf(stderr,"ionil %d ne %d itotc %d link_at %d mult %d\n",
-+                   ionil,ne,jobcom->itotc,link_at,jobcom->imult);
++                   ionil,ne,*itotc,link_at,*imult);
  */
--   ne = ne - jobcom->itotc + linkat;
-+   ne = ne - jobcom->itotc + link_at;
-    if (ne % 2 == jobcom->imult % 2) return(1);
+-   ne = ne - *itotc + linkat;
++   ne = ne - *itotc + link_at;
+    if (ne % 2 == *imult % 2) return(1);
     return(0);
  }
diff --git a/biology/molden/pkg-plist b/biology/molden/pkg-plist
index 169d1e39d52a..53b0cc1ff4b6 100644
--- a/biology/molden/pkg-plist
+++ b/biology/molden/pkg-plist
@@ -5,56 +5,56 @@ bin/surf
 %%PORTDOCS%%%%DOCSDIR%%/manual.txt.Z
 %%PORTDOCS%%%%DOCSDIR%%/manual.ps.Z
 %%PORTDOCS%%%%DOCSDIR%%/figures.ps.Z
-share/molden/test/adf.molf
-share/molden/test/ambfor_amber.xyz
-share/molden/test/ambfor_gaff.xyz
-share/molden/test/ampac.arc
-share/molden/test/ampac.test
-share/molden/test/bucky.xyz
-share/molden/test/chemx.test
-share/molden/test/complex2.out
-share/molden/test/cpeptide.gro
-share/molden/test/esp.test
-share/molden/test/esp.txt
-share/molden/test/esp.xyz
-share/molden/test/fragment
-share/molden/test/gamess_uk.freq
-share/molden/test/gamess_uk.input
-share/molden/test/gamess_uk.test1
-share/molden/test/gamess_uk.test2
-share/molden/test/gamess_us.h2o_631g_opt.out
-share/molden/test/gamess_us.irc
-share/molden/test/gamess_us_uhf_opt
-share/molden/test/gaussian.freq
-share/molden/test/gaussian.input
-share/molden/test/gaussian.test
-share/molden/test/jaguar.cube
-share/molden/test/molden.ogl
-share/molden/test/mopac.freq
-share/molden/test/mopac.test
-share/molden/test/pdb.test
-share/molden/test/pdb.test.omap
-share/molden/test/qchem.test
-share/molden/test/reacpth.xyz
-share/molden/test/shelx.ins
-share/molden/test/surface.molf
-share/molden/test/test.fdat
-share/molden/test/test.mol2
-share/molden/test/test_homo.cube
-share/molden/test/tinker_charmm.xyz
-share/molden/test/tinker_mm3.xyz
-share/molden/test/uracil.fdat
-share/molden/test/uracil_gauss.out
-share/molden/test/vamp.test
-share/molden/utils/INFO
-share/molden/utils/ch_backspace
-share/molden/utils/ch_mxcon
-share/molden/utils/ch_par
-share/molden/utils/colors
-share/molden/utils/ircextract.awk
-share/molden/utils/molden
-share/molden/utils/multi_vrml.csh
-share/molden/utils/multi_vrml_orbitals.csh
-@dirrm share/molden/utils
-@dirrm share/molden/test
-@dirrm share/molden
+%%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%%