Date: Wed, 26 Sep 2012 02:21:01 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/171970: biology/molden: Update to version 6.0 Message-ID: <20120926022101.4f361da137bfaa9c09ef63b8@yahoo.com> Resent-Message-ID: <201209251810.q8PIADsA017740@freefall.freebsd.org>
next in thread | raw e-mail | index | archive | help
>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@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: >Unformatted:
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?20120926022101.4f361da137bfaa9c09ef63b8>