From owner-svn-ports-all@FreeBSD.ORG Sat Dec 1 00:00:43 2012 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [69.147.83.52]) by hub.freebsd.org (Postfix) with ESMTP id EB0959ED; Sat, 1 Dec 2012 00:00:43 +0000 (UTC) (envelope-from sperber@FreeBSD.org) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) by mx1.freebsd.org (Postfix) with ESMTP id D00AB8FC0C; Sat, 1 Dec 2012 00:00:43 +0000 (UTC) Received: from svn.freebsd.org (localhost [127.0.0.1]) by svn.freebsd.org (8.14.5/8.14.5) with ESMTP id qB100hfY082531; Sat, 1 Dec 2012 00:00:43 GMT (envelope-from sperber@svn.freebsd.org) Received: (from sperber@localhost) by svn.freebsd.org (8.14.5/8.14.5/Submit) id qB100huw082519; Sat, 1 Dec 2012 00:00:43 GMT (envelope-from sperber@svn.freebsd.org) Message-Id: <201212010000.qB100huw082519@svn.freebsd.org> From: Armin Pirkovitsch Date: Sat, 1 Dec 2012 00:00:43 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r308054 - in head/biology/tinker: . files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 01 Dec 2012 00:00:44 -0000 Author: sperber Date: Sat Dec 1 00:00:43 2012 New Revision: 308054 URL: http://svnweb.freebsd.org/changeset/ports/308054 Log: - Update to version 6.1.01 - Add MAKE_JOBS_SAFE - Convert to optionsng - Trim Makefile header PR: ports/171971 Submitted by: KATO Tsuguru Approved by: beat (mentor) Feature safe: yes Added: head/biology/tinker/files/patch-bench__bench1.run (contents, props changed) head/biology/tinker/files/patch-bench__bench2.run (contents, props changed) head/biology/tinker/files/patch-bench__bench3.run (contents, props changed) head/biology/tinker/files/patch-bench__bench4.run (contents, props changed) head/biology/tinker/files/patch-bench__bench5.run (contents, props changed) head/biology/tinker/files/patch-make__Makefile (contents, props changed) head/biology/tinker/files/patch-source_openend.f (contents, props changed) head/biology/tinker/files/pkg-message.in (contents, props changed) Deleted: head/biology/tinker/files/patch-aa head/biology/tinker/files/patch-ah head/biology/tinker/files/patch-ai head/biology/tinker/files/patch-aj head/biology/tinker/files/patch-ak head/biology/tinker/files/patch-al head/biology/tinker/files/patch-openend.f Modified: head/biology/tinker/Makefile (contents, props changed) head/biology/tinker/distinfo (contents, props changed) head/biology/tinker/pkg-plist (contents, props changed) Modified: head/biology/tinker/Makefile ============================================================================== --- head/biology/tinker/Makefile Sat Dec 1 00:00:33 2012 (r308053) +++ head/biology/tinker/Makefile Sat Dec 1 00:00:43 2012 (r308054) @@ -1,76 +1,74 @@ -# New ports collection makefile for: tinker -# Date Created: 26 August 1998 -# Whom: Glenn Johnson -# +# Created by: Glenn Johnson # $FreeBSD$ -# PORTNAME= tinker -PORTVERSION= 5.1.09 +PORTVERSION= 6.1.01 CATEGORIES= biology MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/ MAINTAINER= ports@FreeBSD.org COMMENT= A general purpose molecular modelling package -MAKE_ENV+= HAVE_G2C=yes INSTALL_PROGRAM="${INSTALL_PROGRAM}" +RESTRICTED= author requests no distribution except from his FTP site -WRKSRC= ${WRKDIR}/tinker/source +OPTIONS_DEFINE= OPTIMIZED_FFLAGS DATA DOCS EXAMPLES +OPTIONS_DEFAULT=DATA +OPTIMIZED_FFLAGS_DESC= compilation optimizations + +WRKSRC= ${WRKDIR}/${PORTNAME} +BUILD_WRKSRC= ${WRKSRC}/source +INSTALL_WRKSRC= ${WRKSRC}/source -MAKEFILE= ${WRKDIR}/tinker/make/Makefile +USE_FORTRAN= yes +MAKE_ENV= HAVE_G2C=yes +MAKEFILE= ${WRKSRC}/make/Makefile ALL_TARGET= all listing INSTALL_TARGET= rename -RESTRICTED= author requests no distribution except from his FTP site +MAKE_JOBS_SAFE= yes + +SUB_FILES= pkg-message -DOCS= 0README *.pdf *.txt announce/release* -SAMPLES= 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.run *.xyz +DOCS= 0README *.pdf *.txt +SAMPLES= 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz BENCHES= 0README *.dyn0 *.log *.key *.run *.xyz results* .include -USE_FORTRAN= yes - -.if defined(WITH_OPTIMIZED_FLAGS) +.if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS} FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations .if (${ARCH} == "i386") FFLAGS+= -mfancy-math-387 -malign-double .endif # i386 .endif -pre-everything:: -.if !defined(WITH_OPTIMIZED_FLAGS) - @${ECHO_MSG} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes." +.if empty(PORT_OPTIONS:MDATA) +NOPORTDATA= yes .endif post-extract: - ${CHMOD} -R u+w ${WRKDIR}/tinker - -post-patch: - @${REINPLACE_CMD} -e 's|%%FFLAGS%%|${FFLAGS}|g' ${WRKSRC}/../make/Makefile + @${CHMOD} -R u+w ${WRKSRC} post-install: + @${MKDIR} ${DATADIR} + ${INSTALL_DATA} ${INSTALL_WRKSRC}/tinker.txt ${DATADIR} @${MKDIR} ${DATADIR}/params - @${INSTALL_DATA} ${WRKDIR}/tinker/source/tinker.txt \ - ${DATADIR} - @${INSTALL_DATA} ${WRKDIR}/tinker/params/* \ - ${DATADIR}/params -.if !defined(NOPORTDOCS) - @${MKDIR} ${DOCSDIR} - @${MKDIR} ${EXAMPLESDIR} + ${INSTALL_DATA} ${WRKSRC}/params/* ${DATADIR}/params +.if ${PORT_OPTIONS:MDATA} @${MKDIR} ${DATADIR}/bench + ${INSTALL_DATA} ${BENCHES:S|^|${WRKSRC}/bench/|} ${DATADIR}/bench @${MKDIR} ${DATADIR}/test - @${INSTALL_DATA} ${DOCS:S|^|${WRKDIR}/tinker/doc/|} ${DOCSDIR} - @${INSTALL_DATA} ${SAMPLES:S|^|${WRKDIR}/tinker/example/|} ${EXAMPLESDIR} - @${INSTALL_DATA} ${BENCHES:S|^|${WRKDIR}/tinker/bench/|} ${DATADIR}/bench - @${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${DATADIR}/test + ${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test +.endif +.if ${PORT_OPTIONS:MDOCS} + @${MKDIR} ${DOCSDIR} + ${INSTALL_DATA} ${DOCS:S|^|${WRKSRC}/doc/|} ${DOCSDIR} +.endif +.if ${PORT_OPTIONS:MEXAMPLES} + @${MKDIR} ${EXAMPLESDIR} + ${INSTALL_DATA} ${SAMPLES:S|^|${WRKSRC}/example/|} ${EXAMPLESDIR} .endif - @${ECHO_MSG} "" - @${ECHO_MSG} " **********************************************************" - @${ECHO_MSG} " The author requests that you return a license form " - @${ECHO_MSG} " to him if you find Tinker to be useful. " - @${ECHO_MSG} " " - @${ECHO_MSG} " See ${DOCSDIR} for license forms. " - @${ECHO_MSG} " **********************************************************" - @${ECHO_MSG} "" + @${ECHO_CMD} + @${CAT} ${PKGMESSAGE} + @${ECHO_CMD} .include Modified: head/biology/tinker/distinfo ============================================================================== --- head/biology/tinker/distinfo Sat Dec 1 00:00:33 2012 (r308053) +++ head/biology/tinker/distinfo Sat Dec 1 00:00:43 2012 (r308054) @@ -1,2 +1,2 @@ -SHA256 (tinker-5.1.09.tar.gz) = 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183 -SIZE (tinker-5.1.09.tar.gz) = 14071638 +SHA256 (tinker-6.1.01.tar.gz) = fa287c381fd866822b19396fa152406b8463421f0a27902867cdbbf6b67233e4 +SIZE (tinker-6.1.01.tar.gz) = 19478639 Added: head/biology/tinker/files/patch-bench__bench1.run ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tinker/files/patch-bench__bench1.run Sat Dec 1 00:00:43 2012 (r308054) @@ -0,0 +1,5 @@ +--- bench/bench1.run.orig Tue Jul 24 14:02:20 2001 ++++ bench/bench1.run Wed Sep 5 13:57:02 2001 +@@ -1 +1 @@ +-../bin/timer bench1 1 y ++timer bench1 1 y Added: head/biology/tinker/files/patch-bench__bench2.run ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tinker/files/patch-bench__bench2.run Sat Dec 1 00:00:43 2012 (r308054) @@ -0,0 +1,5 @@ +--- bench/bench2.run.orig Tue Jul 24 14:02:20 2001 ++++ bench/bench2.run Wed Sep 5 13:58:47 2001 +@@ -1 +1 @@ +-../bin/timer bench2 1 y ++timer bench2 1 y Added: head/biology/tinker/files/patch-bench__bench3.run ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tinker/files/patch-bench__bench3.run Sat Dec 1 00:00:43 2012 (r308054) @@ -0,0 +1,5 @@ +--- bench/bench3.run.orig Wed Sep 5 14:00:09 2001 ++++ bench/bench3.run Wed Sep 5 14:01:27 2001 +@@ -1 +1 @@ +-time ../bin/vibrate bench3 0 ++time vibrate bench3 0 Added: head/biology/tinker/files/patch-bench__bench4.run ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tinker/files/patch-bench__bench4.run Sat Dec 1 00:00:43 2012 (r308054) @@ -0,0 +1,7 @@ +--- bench/bench4.run.orig Tue Jul 24 14:02:20 2001 ++++ bench/bench4.run Wed Sep 5 14:02:17 2001 +@@ -1,3 +1,3 @@ + cp bench4.dyn0 bench4.dyn +-time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0 ++time dynamic bench4 1000 1.0 10.0 2 298.0 + rm bench4.dyn Added: head/biology/tinker/files/patch-bench__bench5.run ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tinker/files/patch-bench__bench5.run Sat Dec 1 00:00:43 2012 (r308054) @@ -0,0 +1,7 @@ +--- bench/bench5.run.orig 2010-08-25 00:58:15.000000000 +0400 ++++ bench/bench5.run 2011-01-26 23:35:18.000000000 +0300 +@@ -1,3 +1,3 @@ + cp bench5.dyn0 bench5.dyn +-time ../bin/dynamic bench5 1000 1.0 10.0 2 298.0 ++time dynamic bench5 1000 1.0 10.0 2 298.0 + rm bench5.dyn Added: head/biology/tinker/files/patch-make__Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tinker/files/patch-make__Makefile Sat Dec 1 00:00:43 2012 (r308054) @@ -0,0 +1,211 @@ +--- make/Makefile.orig 2012-06-29 14:51:42.000000000 +0900 ++++ make/Makefile 2012-11-10 00:12:19.000000000 +0900 +@@ -9,8 +9,8 @@ + ## + ## 1. make all Build all the TINKER executables + ## 2. make rename Move the executables to BINDIR +-## 3. make remove_links Create soft links in LINKDIR +-## 4. make create_links Remove soft links from LINKDIR ++## 3. make remove_links Remove soft links in LINKDIR ++## 4. make create_links Create soft links from LINKDIR + ## 6. make listing Concatenate source to tinker.txt + ## 5. make clean Delete objects and executables + ## +@@ -30,9 +30,9 @@ + ## LINKDIR Linked Copies of TINKER Executables + ## + +-TINKERDIR = /Users/ponder/tinker +-BINDIR = $(TINKERDIR)/bin +-LINKDIR = /usr/local/bin ++TINKERDIR = ${WRKDIR} ++BINDIR = ${PREFIX}/bin ++#LINKDIR = /usr/local/bin + + #################################################################### + ## Known Machine Types; Uncomment One of the Following Sections ## +@@ -40,6 +40,20 @@ + #################################################################### + + ## ++## Machine: IntelPC / FreeBSD ++## CPU Type: Intel, AMD, Cyrix ++## Oper Sys: FreeBSD 4.2 ++## Compiler: f77 , aka g77 ++## ++ ++F77 = ${FC} ++LIBS = ++F77FLAGS = -c ${FFLAGS} ++LINKFLAGS = ${LDFLAGS} ++OPTFLAGS = ++LIBFLAGS = -rcuv ++ ++## + ## Machine: Generic Linux + ## CPU Type: Intel x86 Compatible + ## Oper Sys: Fedora Core +@@ -104,12 +118,12 @@ + ## Parallel: OpenMP + ## + +-F77 = /opt/intel/bin/ifort +-LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3 +-F77FLAGS = -c -axSSSE3 -assume cc_omp +-OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp +-LIBFLAGS = -crusv +-LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4 ++#F77 = /opt/intel/bin/ifort ++#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3 ++#F77FLAGS = -c -axSSSE3 -assume cc_omp ++#OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp ++#LIBFLAGS = -crusv ++#LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4 + + ## + ## Machine: Macintosh +@@ -592,6 +606,8 @@ + xyzpdb.x \ + xyzsybyl.x + ++.SUFFIXES: .x ++ + .f.o: + ${F77} ${F77FLAGS} ${OPTFLAGS} $*.f + +@@ -601,8 +617,8 @@ + server.o: + ${F77} ${F77FLAGS} ${OPTFLAGS} server.f + +-%.x: %.o libtinker.a +- ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@ ++.o.x: libtinker.a ++ ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS} + + all: ${EXEFILES} + +@@ -613,65 +629,65 @@ + cat *.i *.f *.c > tinker.txt + + rename: +- mv alchemy.x $(BINDIR)/alchemy +- mv analyze.x $(BINDIR)/analyze +- mv anneal.x $(BINDIR)/anneal +- mv archive.x $(BINDIR)/archive +- mv correlate.x $(BINDIR)/correlate +- mv crystal.x $(BINDIR)/crystal +- mv diffuse.x $(BINDIR)/diffuse +- mv distgeom.x $(BINDIR)/distgeom +- mv document.x $(BINDIR)/document +- mv dynamic.x $(BINDIR)/dynamic +- mv gda.x $(BINDIR)/gda +- mv intedit.x $(BINDIR)/intedit +- mv intxyz.x $(BINDIR)/intxyz +- mv minimize.x $(BINDIR)/minimize +- mv minirot.x $(BINDIR)/minirot +- mv minrigid.x $(BINDIR)/minrigid +- mv molxyz.x $(BINDIR)/molxyz +- mv monte.x $(BINDIR)/monte +- mv newton.x $(BINDIR)/newton +- mv newtrot.x $(BINDIR)/newtrot +- mv nucleic.x $(BINDIR)/nucleic +- mv optimize.x $(BINDIR)/optimize +- mv optirot.x $(BINDIR)/optirot +- mv optrigid.x $(BINDIR)/optrigid +- mv path.x $(BINDIR)/path +- mv pdbxyz.x $(BINDIR)/pdbxyz +- mv polarize.x $(BINDIR)/polarize +- mv poledit.x $(BINDIR)/poledit +- mv potential.x $(BINDIR)/potential +- mv prmedit.x $(BINDIR)/prmedit +- mv protein.x $(BINDIR)/protein +- mv pss.x $(BINDIR)/pss +- mv pssrigid.x $(BINDIR)/pssrigid +- mv pssrot.x $(BINDIR)/pssrot +- mv radial.x $(BINDIR)/radial +- mv saddle.x $(BINDIR)/saddle +- mv scan.x $(BINDIR)/scan +- mv sniffer.x $(BINDIR)/sniffer +- mv spacefill.x $(BINDIR)/spacefill +- mv spectrum.x $(BINDIR)/spectrum +- mv superpose.x $(BINDIR)/superpose +- mv sybylxyz.x $(BINDIR)/sybylxyz +- mv testgrad.x $(BINDIR)/testgrad +- mv testhess.x $(BINDIR)/testhess +- mv testpair.x $(BINDIR)/testpair +- mv testrot.x $(BINDIR)/testrot +- mv timer.x $(BINDIR)/timer +- mv timerot.x $(BINDIR)/timerot +- mv torsfit.x $(BINDIR)/torsfit +- mv valence.x $(BINDIR)/valence +- mv vibbig.x $(BINDIR)/vibbig +- mv vibrate.x $(BINDIR)/vibrate +- mv vibrot.x $(BINDIR)/vibrot +- mv xtalfit.x $(BINDIR)/xtalfit +- mv xtalmin.x $(BINDIR)/xtalmin +- mv xyzedit.x $(BINDIR)/xyzedit +- mv xyzint.x $(BINDIR)/xyzint +- mv xyzpdb.x $(BINDIR)/xyzpdb +- mv xyzsybyl.x $(BINDIR)/xyzsybyl ++ ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy ++ ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze ++ ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal ++ ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive ++ ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate ++ ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal ++ ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse ++ ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom ++ ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document ++ ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic ++ ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda ++ ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit ++ ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz ++ ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize ++ ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot ++ ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid ++ ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz ++ ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte ++ ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton ++ ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot ++ ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic ++ ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize ++ ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot ++ ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid ++ ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path ++ ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz ++ ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize ++ ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit ++ ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential ++ ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit ++ ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein ++ ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss ++ ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid ++ ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot ++ ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial ++ ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle ++ ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan ++ ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer ++ ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill ++ ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum ++ ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose ++ ${BSD_INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz ++ ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad ++ ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess ++ ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair ++ ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot ++ ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer ++ ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot ++ ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit ++ ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence ++ ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig ++ ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate ++ ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot ++ ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit ++ ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin ++ ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit ++ ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint ++ ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb ++ ${BSD_INSTALL_PROGRAM} xyzsybyl.x $(BINDIR)/xyzsybyl + + remove_links: + rm -f $(LINKDIR)/alchemy Added: head/biology/tinker/files/patch-source_openend.f ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tinker/files/patch-source_openend.f Sat Dec 1 00:00:43 2012 (r308054) @@ -0,0 +1,19 @@ + +$FreeBSD$ + +--- source/openend.f.orig Fri Apr 18 13:31:51 2003 ++++ source/openend.f Mon Jul 21 13:36:11 2003 +@@ -29,11 +29,11 @@ + c + c standard Fortran 90, unavailable in some Fortran 77 compilers + c +- open (unit=iunit,file=name,status='old',position='append') ++c open (unit=iunit,file=name,status='old',position='append') + c + c common extension supported by many Fortran 77 compilers + c +-c open (unit=iunit,file=name,status='old',access='append') ++ open (unit=iunit,file=name,status='old',access='append') + c + c some Fortran 77 compilers open files for append by default + c Added: head/biology/tinker/files/pkg-message.in ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/tinker/files/pkg-message.in Sat Dec 1 00:00:43 2012 (r308054) @@ -0,0 +1,6 @@ +********************************************************** + The author requests that you return a license form + to him if you find Tinker to be useful. + + See %%DOCSDIR%% for license forms. +**********************************************************" Modified: head/biology/tinker/pkg-plist ============================================================================== --- head/biology/tinker/pkg-plist Sat Dec 1 00:00:33 2012 (r308053) +++ head/biology/tinker/pkg-plist Sat Dec 1 00:00:43 2012 (r308054) @@ -14,6 +14,7 @@ bin/intxyz bin/minimize bin/minirot bin/minrigid +bin/molxyz bin/monte bin/newton bin/newtrot @@ -45,6 +46,7 @@ bin/testpair bin/testrot bin/timer bin/timerot +bin/torsfit bin/valence bin/vibbig bin/vibrate @@ -58,424 +60,429 @@ bin/xyzsybyl %%PORTDOCS%%%%DOCSDIR%%/0README %%PORTDOCS%%%%DOCSDIR%%/ffe-guide.pdf %%PORTDOCS%%%%DOCSDIR%%/guide.pdf -%%PORTDOCS%%%%DOCSDIR%%/guide.txt %%PORTDOCS%%%%DOCSDIR%%/license.pdf %%PORTDOCS%%%%DOCSDIR%%/license.txt -%%PORTDOCS%%%%DOCSDIR%%/release-3.2 -%%PORTDOCS%%%%DOCSDIR%%/release-3.6 -%%PORTDOCS%%%%DOCSDIR%%/release-3.7 -%%PORTDOCS%%%%DOCSDIR%%/release-3.8 -%%PORTDOCS%%%%DOCSDIR%%/release-3.9 -%%PORTDOCS%%%%DOCSDIR%%/release-4.0 -%%PORTDOCS%%%%DOCSDIR%%/release-4.1 -%%PORTDOCS%%%%DOCSDIR%%/release-4.2 %%PORTDOCS%%%%DOCSDIR%%/summary.pdf %%PORTDOCS%%%%DOCSDIR%%/summary.txt -%%PORTDOCS%%%%EXAMPLESDIR%%/0README -%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.int -%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.key -%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.seq -%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/alkane.key -%%PORTDOCS%%%%EXAMPLESDIR%%/alkane.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/ammonia.key -%%PORTDOCS%%%%EXAMPLESDIR%%/ammonia.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/amoeba.key -%%PORTDOCS%%%%EXAMPLESDIR%%/amoeba.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/arach.int -%%PORTDOCS%%%%EXAMPLESDIR%%/arach.key -%%PORTDOCS%%%%EXAMPLESDIR%%/arach.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.int -%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.key -%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.int -%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.key -%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.make -%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.pdb -%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.seq -%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/bearing.key -%%PORTDOCS%%%%EXAMPLESDIR%%/bearing.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/bearing2.key -%%PORTDOCS%%%%EXAMPLESDIR%%/benzamidine.key -%%PORTDOCS%%%%EXAMPLESDIR%%/benzamidine.xyz -%%PORTDOCS%%%%EXAMPLESDIR%%/benzbox.key -%%PORTDOCS%%%%EXAMPLESDIR%%/benzbox.xyz 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+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/book.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/book.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl2.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl2.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl3.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl3.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.dyn +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanex.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanex.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cage.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cage.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.pdb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cawater.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cawater.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.make +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.pdb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.pdb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cycprop.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cycprop.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dang.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dang.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.make +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.pdb +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diamond.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diamond.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dimethane.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dimethane.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dmp.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dmp.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.make +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.seq +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ester.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ester.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.int +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethanol.int *** DIFF OUTPUT TRUNCATED AT 1000 LINES ***