From owner-svn-ports-all@FreeBSD.ORG Sun Jan 4 15:21:14 2015 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id D704F27F; Sun, 4 Jan 2015 15:21:14 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id B93AB649AD; Sun, 4 Jan 2015 15:21:14 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.9/8.14.9) with ESMTP id t04FLE5x085563; Sun, 4 Jan 2015 15:21:14 GMT (envelope-from pi@FreeBSD.org) Received: (from pi@localhost) by svn.freebsd.org (8.14.9/8.14.9/Submit) id t04FLDSA085557; Sun, 4 Jan 2015 15:21:13 GMT (envelope-from pi@FreeBSD.org) Message-Id: <201501041521.t04FLDSA085557@svn.freebsd.org> X-Authentication-Warning: svn.freebsd.org: pi set sender to pi@FreeBSD.org using -f From: Kurt Jaeger Date: Sun, 4 Jan 2015 15:21:13 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r376238 - 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: 2.1.18-1 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: Sun, 04 Jan 2015 15:21:15 -0000 Author: pi Date: Sun Jan 4 15:21:12 2015 New Revision: 376238 URL: https://svnweb.freebsd.org/changeset/ports/376238 QAT: https://qat.redports.org/buildarchive/r376238/ Log: biology/tinker: 6.2.6 -> 7.0.1 PR: 196376 Submitted by: Nikola Kolev Modified: head/biology/tinker/Makefile head/biology/tinker/distinfo head/biology/tinker/files/patch-bench__bench4.run head/biology/tinker/files/patch-bench__bench5.run head/biology/tinker/files/patch-make__Makefile head/biology/tinker/pkg-plist Modified: head/biology/tinker/Makefile ============================================================================== --- head/biology/tinker/Makefile Sun Jan 4 15:05:06 2015 (r376237) +++ head/biology/tinker/Makefile Sun Jan 4 15:21:12 2015 (r376238) @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= tinker -PORTVERSION= 6.2.6 -PORTREVISION= 6 +PORTVERSION= 7.0.1 CATEGORIES= biology MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/ @@ -27,9 +26,11 @@ INSTALL_WRKSRC= ${WRKSRC}/source USES= fortran MAKE_ENV= HAVE_G2C=yes MAKEFILE= ${WRKSRC}/make/Makefile -ALL_TARGET= all listing +ALL_TARGET= all INSTALL_TARGET= rename +MAKE_JOBS_UNSAFE=yes + SUB_FILES= pkg-message .include @@ -49,10 +50,9 @@ pre-build: post-install: ${MKDIR} ${STAGEDIR}${DATADIR} - (cd ${INSTALL_WRKSRC} && ${INSTALL_DATA} tinker.txt ${STAGEDIR}${DATADIR}) ${MKDIR} ${STAGEDIR}${DATADIR}/bench (cd ${WRKSRC}/bench && ${INSTALL_DATA} \ - 0README *.dyn0 *.log *.key *.run *.xyz results* \ + 0README *.log *.key *.run *.xyz results* \ ${STAGEDIR}${DATADIR}/bench) ${MKDIR} ${STAGEDIR}${DATADIR}/params (cd ${WRKSRC}/params && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/params) Modified: head/biology/tinker/distinfo ============================================================================== --- head/biology/tinker/distinfo Sun Jan 4 15:05:06 2015 (r376237) +++ head/biology/tinker/distinfo Sun Jan 4 15:21:12 2015 (r376238) @@ -1,2 +1,2 @@ -SHA256 (tinker-6.2.6.tar.gz) = a6eb5cb31b7e93a1f2d323ca73e45f16291763a3e0faa3615a3219e6f9814277 -SIZE (tinker-6.2.6.tar.gz) = 20181780 +SHA256 (tinker-7.0.1.tar.gz) = 5c68c097e2843a497224ee58833fb0a816a99529426be612f4dcc5eebd797b1c +SIZE (tinker-7.0.1.tar.gz) = 28384106 Modified: head/biology/tinker/files/patch-bench__bench4.run ============================================================================== --- head/biology/tinker/files/patch-bench__bench4.run Sun Jan 4 15:05:06 2015 (r376237) +++ head/biology/tinker/files/patch-bench__bench4.run Sun Jan 4 15:21:12 2015 (r376238) @@ -1,7 +1,5 @@ ---- 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 +--- bench/bench4.run.orig 2014-12-16 05:17:53.000000000 +0200 ++++ bench/bench4.run 2014-12-28 18:56:02.000000000 +0200 +@@ -1 +1 @@ -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 Modified: head/biology/tinker/files/patch-bench__bench5.run ============================================================================== --- head/biology/tinker/files/patch-bench__bench5.run Sun Jan 4 15:05:06 2015 (r376237) +++ head/biology/tinker/files/patch-bench__bench5.run Sun Jan 4 15:21:12 2015 (r376238) @@ -1,7 +1,5 @@ ---- 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 +--- bench/bench5.run.orig 2014-12-16 05:17:53.000000000 +0200 ++++ bench/bench5.run 2014-12-28 18:58:45.000000000 +0200 +@@ -1 +1 @@ -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 Modified: head/biology/tinker/files/patch-make__Makefile ============================================================================== --- head/biology/tinker/files/patch-make__Makefile Sun Jan 4 15:05:06 2015 (r376237) +++ head/biology/tinker/files/patch-make__Makefile Sun Jan 4 15:21:12 2015 (r376238) @@ -1,10 +1,10 @@ ---- make/Makefile.orig 2013-07-14 11:23:53.000000000 +0900 -+++ make/Makefile 2014-03-14 16:59:17.000000000 +0900 -@@ -30,9 +30,9 @@ +--- make/Makefile.orig 2014-12-16 05:18:02.000000000 +0200 ++++ make/Makefile 2014-12-30 10:29:50.000000000 +0200 +@@ -33,9 +33,9 @@ + ## BINDIR Hard Copies of TINKER Executables ## LINKDIR Linked Copies of TINKER Executables - ## --TINKERDIR = /Users/ponder/tinker +-TINKERDIR = $(HOME)/tinker -BINDIR = $(TINKERDIR)/bin -LINKDIR = /usr/local/bin +TINKERDIR = ${WRKDIR} @@ -13,68 +13,83 @@ #################################################################### ## Known Machine Types; Uncomment One of the Following Sections ## -@@ -40,6 +40,20 @@ - #################################################################### +@@ -46,26 +46,26 @@ LINKDIR = /usr/local/bin + ## CPU Type: Intel x86 Compatible + ## Compiler: GNU gfortran - ## -+## Machine: IntelPC / FreeBSD -+## CPU Type: Intel, AMD, Cyrix -+## Oper Sys: FreeBSD 4.2 -+## Compiler: f77 , aka g77 -+## -+ +-#F77 = gfortran +-#LIBS = +-#F77FLAGS = -c +-#OPTFLAGS = -O3 -ffast-math +-#LIBFLAGS = -crusv +-#RANLIB = ranlib -c +-#LINKFLAGS = $(OPTFLAGS) -static-libgcc +F77 = ${FC} -+LIBS = ++LIBS = +F77FLAGS = -c ${FFLAGS} -+LINKFLAGS = ${LDFLAGS} +OPTFLAGS = +LIBFLAGS = -rcuv -+ -+## - ## Machine: Generic Linux ++RANLIB = ranlib ++LINKFLAGS = ${LDFLAGS} + + ## Machine: Generic Linux or Macintosh ## CPU Type: Intel x86 Compatible - ## Oper Sys: Fedora Core -@@ -104,12 +118,12 @@ + ## Compiler: GNU gfortran ## Parallel: OpenMP - ## --F77 = /opt/intel/bin/ifort --LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3 --F77FLAGS = -c -axSSSE3 -assume cc_omp --OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp +-F77 = gfortran +-LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3 +-F77FLAGS = -c +-OPTFLAGS = -O3 -ffast-math -fopenmp -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 +-RANLIB = ranlib -c +-LINKFLAGS = $(OPTFLAGS) -static-libgcc ++#F77 = gfortran ++#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3 ++#F77FLAGS = -c ++#OPTFLAGS = -O3 -ffast-math -fopenmp +#LIBFLAGS = -crusv -+#LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4 ++#RANLIB = ranlib -c ++#LINKFLAGS = $(OPTFLAGS) -static-libgcc + + ## Machine: Generic Linux + ## CPU Type: Intel x86 Compatible (also AMD) +@@ -106,7 +106,7 @@ LINKFLAGS = $(OPTFLAGS) -static-libgcc + #LIBFLAGS = -crusv + #RANLIB = ranlib -c + #LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.6 \ +- -Wl,-stack_size,0x10000000 ++# -Wl,-stack_size,0x10000000 - ## ## Machine: Macintosh -@@ -597,14 +611,13 @@ + ## CPU Type: Intel Xeon +@@ -710,93 +710,88 @@ EXEFILES = alchemy.x \ xyzpdb.x \ xyzsybyl.x -%.o: %.f - ${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ -+.SUFFIXES: .x - +- -%.o: %.c - ${CC} ${CFLAGS} ${INCLUDEDIR} ${OPTFLAGS} $< -+.f.o: -+ ${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ ++.SUFFIXES: .x -%.x: %.o libtinker.a - ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@ ++.f.o: ++ ${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ + +-all: +- ${EXEFILES} +.o.x: libtinker.a + ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS} - all: ${EXEFILES} +-install: +- rename ++all: ${EXEFILES} -@@ -612,74 +625,74 @@ - rm -f *.o *.a *.x + clean: + rm -f *.o *.mod *.a *.x listing: - cat *.i *.f *.c > tinker.txt @@ -211,7 +226,7 @@ rm -f $(LINKDIR)/anneal rm -f $(LINKDIR)/archive rm -f $(LINKDIR)/bar -@@ -742,7 +755,7 @@ +@@ -859,7 +854,7 @@ remove_links: create_links: ln -s $(BINDIR)/alchemy $(LINKDIR)/alchemy Modified: head/biology/tinker/pkg-plist ============================================================================== --- head/biology/tinker/pkg-plist Sun Jan 4 15:05:06 2015 (r376237) +++ head/biology/tinker/pkg-plist Sun Jan 4 15:21:12 2015 (r376238) @@ -162,8 +162,10 @@ bin/xyzsybyl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin2.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin2.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin3.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin3.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.int %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.xyz @@ -398,6 +400,8 @@ bin/xyzsybyl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4f.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4p.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4p.xyz +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4pbox.key +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4pbox.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip5p.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip5p.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.key @@ -451,14 +455,13 @@ bin/xyzsybyl %%DATADIR%%/bench/bench2.run %%DATADIR%%/bench/bench2.xyz %%DATADIR%%/bench/bench3.key +%%DATADIR%%/bench/bench3.log %%DATADIR%%/bench/bench3.run %%DATADIR%%/bench/bench3.xyz -%%DATADIR%%/bench/bench4.dyn0 %%DATADIR%%/bench/bench4.key %%DATADIR%%/bench/bench4.log %%DATADIR%%/bench/bench4.run %%DATADIR%%/bench/bench4.xyz -%%DATADIR%%/bench/bench5.dyn0 %%DATADIR%%/bench/bench5.key %%DATADIR%%/bench/bench5.log %%DATADIR%%/bench/bench5.run @@ -471,6 +474,14 @@ bin/xyzsybyl %%DATADIR%%/bench/bench7.log %%DATADIR%%/bench/bench7.run %%DATADIR%%/bench/bench7.xyz +%%DATADIR%%/bench/bench8.key +%%DATADIR%%/bench/bench8.log +%%DATADIR%%/bench/bench8.run +%%DATADIR%%/bench/bench8.xyz +%%DATADIR%%/bench/bench9.key +%%DATADIR%%/bench/bench9.log +%%DATADIR%%/bench/bench9.run +%%DATADIR%%/bench/bench9.xyz %%DATADIR%%/bench/results-2.3 %%DATADIR%%/bench/results-2.4 %%DATADIR%%/bench/results-2.9 @@ -489,6 +500,8 @@ bin/xyzsybyl %%DATADIR%%/bench/results-5.1 %%DATADIR%%/bench/results-6.0 %%DATADIR%%/bench/results-6.2 +%%DATADIR%%/bench/results-6.3 +%%DATADIR%%/bench/results-7.0 %%DATADIR%%/params/0README %%DATADIR%%/params/amber94.prm %%DATADIR%%/params/amber96.prm @@ -516,7 +529,8 @@ bin/xyzsybyl %%DATADIR%%/params/smoothaa.prm %%DATADIR%%/params/smoothua.prm %%DATADIR%%/params/tiny.prm -%%DATADIR%%/params/water.prm +%%DATADIR%%/params/water03.prm +%%DATADIR%%/params/water14.prm %%DATADIR%%/test/0README %%DATADIR%%/test/anion.dat %%DATADIR%%/test/anion.dyn0 @@ -593,6 +607,11 @@ bin/xyzsybyl %%DATADIR%%/test/ifabp.log %%DATADIR%%/test/ifabp.run %%DATADIR%%/test/ifabp.xyz +%%DATADIR%%/test/nitrogen.arc +%%DATADIR%%/test/nitrogen.key +%%DATADIR%%/test/nitrogen.log +%%DATADIR%%/test/nitrogen.run +%%DATADIR%%/test/nitrogen.xyz %%DATADIR%%/test/salt.cell %%DATADIR%%/test/salt.key %%DATADIR%%/test/salt.log @@ -606,4 +625,3 @@ bin/xyzsybyl %%DATADIR%%/test/water.pot %%DATADIR%%/test/water.run %%DATADIR%%/test/water.xyz -%%DATADIR%%/tinker.txt