ports/171970: biology/molden: Update to version 6.0
KATO Tsuguru
tkato432 at yahoo.com
Tue Sep 25 18:10:13 UTC 2012
>Number: 171970
>Category: ports
>Synopsis: biology/molden: Update to version 6.0
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Tue Sep 25 18:10:12 UTC 2012
>Closed-Date:
>Last-Modified:
>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 at 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%%
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