Date: Mon, 31 Dec 2001 22:39:12 -0600 (CST) From: Glenn Johnson <glennpj@charter.net> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/33425: maintainer update: biology/tinker Message-ID: <200201010439.g014dC172387@gforce.johnson.home>
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>Number: 33425 >Category: ports >Synopsis: maintainer update: biology/tinker >Confidential: no >Severity: non-critical >Priority: high >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Mon Dec 31 20:40:00 PST 2001 >Closed-Date: >Last-Modified: >Originator: Glenn Johnson >Release: FreeBSD 4.5-PRERELEASE i386 >Organization: >Environment: System: FreeBSD gforce.johnson.home 4.5-PRERELEASE FreeBSD 4.5-PRERELEASE #3: Sun Dec 30 16:10:30 CST 2001 root@gforce.johnson.home:/usr/obj/usr/src/sys/GFORCE i386 >Description: Upgrade tinker to the latest revision >How-To-Repeat: >Fix: Apply the attached patch diff -ruN tinker.old/Makefile tinker/Makefile --- tinker.old/Makefile Mon Dec 31 14:45:33 2001 +++ tinker/Makefile Mon Dec 31 20:56:27 2001 @@ -7,6 +7,7 @@ PORTNAME= tinker PORTVERSION= 3.9 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://dasher.wustl.edu/pub/ DISTNAME= ${PORTNAME} @@ -28,7 +29,7 @@ @${ECHO_MSG} If you get a CHECKSUM mismatch, try doing a \'make distclean\' first. @${ECHO_MSG} "" -.if defined(WANT_VIEWER) +.if defined(WITH_VIEWER) .if ${XFREE86_VERSION} == 3 BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake .elif ${XFREE86_VERSION} == 4 @@ -42,7 +43,7 @@ pre-extract: @${ECHO} "" @${ECHO} If you would like to also build - @${ECHO} the molecular viewer, define WANT_VIEWER. + @${ECHO} the molecular viewer, define WITH_VIEWER. @${ECHO} "" .endif @@ -114,7 +115,7 @@ @${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${PREFIX}/share/tinker/test .endif -.if defined(WANT_VIEWER) +.if defined(WITH_VIEWER) @${MKDIR} ${PREFIX}/share/tinker/rasmol @${INSTALL_PROGRAM} ${WRKDIR}/tinker/rasmol/tview-* ${PREFIX}/bin @${INSTALL_SCRIPT} ${FILESDIR}/tview ${PREFIX}/bin diff -ruN tinker.old/distinfo tinker/distinfo --- tinker.old/distinfo Mon Dec 31 14:45:33 2001 +++ tinker/distinfo Mon Dec 31 20:56:27 2001 @@ -1 +1 @@ -MD5 (tinker.tar.gz) = a48fc15fe668f8e41d0cc3316a582928 +MD5 (tinker.tar.gz) = e6f34c61cc40f107fbbcf4b0c7dae5a5 diff -ruN tinker.old/files/patch-aa tinker/files/patch-aa --- tinker.old/files/patch-aa Mon Dec 31 14:45:33 2001 +++ tinker/files/patch-aa Mon Dec 31 20:56:27 2001 @@ -1,5 +1,5 @@ ---- ../make/Makefile.orig Sat Jul 21 10:04:48 2001 -+++ ../make/Makefile Wed Sep 5 13:51:19 2001 +--- ../make/Makefile.orig Tue Nov 13 10:16:27 2001 ++++ ../make/Makefile Mon Dec 31 15:33:40 2001 @@ -9,8 +9,8 @@ ## ## 1. make all Build all the TINKER executables @@ -68,7 +68,7 @@ ################################################################# ## Should not be Necessary to Change Things Below this Point ## ################################################################# -@@ -494,11 +512,13 @@ +@@ -497,11 +515,13 @@ xyzpdb.x \ xyzsybyl.x @@ -84,7 +84,7 @@ all: ${EXEFILES} -@@ -509,57 +529,57 @@ +@@ -512,58 +532,58 @@ cat *.i *.f > tinker.txt rename: @@ -104,6 +104,7 @@ - mv minimize.x $(BINDIR)/minimize - mv minirot.x $(BINDIR)/minirot - mv minrigid.x $(BINDIR)/minrigid +- mv monte.x $(BINDIR)/monte - mv newton.x $(BINDIR)/newton - mv newtrot.x $(BINDIR)/newtrot - mv nucleic.x $(BINDIR)/nucleic @@ -155,6 +156,7 @@ + ${INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize + ${INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot + ${INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid ++ ${INSTALL_PROGRAM} monte.x $(BINDIR)/monte + ${INSTALL_PROGRAM} newton.x $(BINDIR)/newton + ${INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot + ${INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic @@ -193,13 +195,3 @@ remove_links: rm -f $(LINKDIR)/alchemy -@@ -682,8 +702,8 @@ - bspline.o \ - calendar.o \ - center.o \ -- chkxyz.o \ - cholesky.o \ -+ chkxyz.o \ - clock.o \ - cluster.o \ - column.o \ diff -ruN tinker.old/pkg-plist tinker/pkg-plist --- tinker.old/pkg-plist Mon Dec 31 14:45:33 2001 +++ tinker/pkg-plist Mon Dec 31 20:58:51 2001 @@ -14,6 +14,7 @@ bin/minimize bin/minirot bin/minrigid +bin/monte bin/newton bin/newtrot bin/nucleic @@ -139,19 +140,18 @@ %%PORTDOCS%%share/tinker/bench/results-3.7 %%PORTDOCS%%share/tinker/bench/results-3.8 %%PORTDOCS%%share/tinker/bench/results-3.9 -%%PORTDOCS%%share/tinker/params/README -%%PORTDOCS%%share/tinker/params/amber.prm -%%PORTDOCS%%share/tinker/params/charmm.prm -%%PORTDOCS%%share/tinker/params/dudek.prm -%%PORTDOCS%%share/tinker/params/hoch.prm -%%PORTDOCS%%share/tinker/params/mm2.prm -%%PORTDOCS%%share/tinker/params/mm3.prm -%%PORTDOCS%%share/tinker/params/mm3pro.prm -%%PORTDOCS%%share/tinker/params/opls.prm -%%PORTDOCS%%share/tinker/params/oplsaa.prm -%%PORTDOCS%%share/tinker/params/smooth.prm -%%PORTDOCS%%share/tinker/params/smoothaa.prm -%%PORTDOCS%%share/tinker/params/water.prm +share/tinker/params/README +share/tinker/params/amber.prm +share/tinker/params/charmm.prm +share/tinker/params/hoch.prm +share/tinker/params/mm2.prm +share/tinker/params/mm3.prm +share/tinker/params/mm3pro.prm +share/tinker/params/opls.prm +share/tinker/params/oplsaa.prm +share/tinker/params/smooth.prm +share/tinker/params/smoothaa.prm +share/tinker/params/water.prm %%PORTDOCS%%share/tinker/test/README %%PORTDOCS%%share/tinker/test/ala20.key %%PORTDOCS%%share/tinker/test/ala20.xyz @@ -182,6 +182,9 @@ %%PORTDOCS%%share/tinker/test/bowl2.xyz %%PORTDOCS%%share/tinker/test/bowl3.key %%PORTDOCS%%share/tinker/test/bowl3.xyz +%%PORTDOCS%%share/tinker/test/bucky.int +%%PORTDOCS%%share/tinker/test/bucky.key +%%PORTDOCS%%share/tinker/test/bucky.xyz %%PORTDOCS%%share/tinker/test/butane.int %%PORTDOCS%%share/tinker/test/butane.key %%PORTDOCS%%share/tinker/test/butane.xyz @@ -202,12 +205,12 @@ %%PORTDOCS%%share/tinker/test/c5.key %%PORTDOCS%%share/tinker/test/c5.seq %%PORTDOCS%%share/tinker/test/c5.xyz -%%PORTDOCS%%share/tinker/test/c7ax.key -%%PORTDOCS%%share/tinker/test/c7ax.seq -%%PORTDOCS%%share/tinker/test/c7ax.xyz -%%PORTDOCS%%share/tinker/test/c7eq.key -%%PORTDOCS%%share/tinker/test/c7eq.seq -%%PORTDOCS%%share/tinker/test/c7eq.xyz +%%PORTDOCS%%share/tinker/test/c7a.key +%%PORTDOCS%%share/tinker/test/c7a.seq +%%PORTDOCS%%share/tinker/test/c7a.xyz +%%PORTDOCS%%share/tinker/test/c7e.key +%%PORTDOCS%%share/tinker/test/c7e.seq +%%PORTDOCS%%share/tinker/test/c7e.xyz %%PORTDOCS%%share/tinker/test/calmodulin.key %%PORTDOCS%%share/tinker/test/calmodulin.pdb %%PORTDOCS%%share/tinker/test/calmodulin.seq @@ -245,6 +248,9 @@ %%PORTDOCS%%share/tinker/test/diene.xyz %%PORTDOCS%%share/tinker/test/dimethane.key %%PORTDOCS%%share/tinker/test/dimethane.xyz +%%PORTDOCS%%share/tinker/test/diwater.key +%%PORTDOCS%%share/tinker/test/diwater.lin +%%PORTDOCS%%share/tinker/test/diwater.xyz %%PORTDOCS%%share/tinker/test/enkephalin.int %%PORTDOCS%%share/tinker/test/enkephalin.key %%PORTDOCS%%share/tinker/test/enkephalin.make @@ -271,6 +277,7 @@ %%PORTDOCS%%share/tinker/test/form.xyz %%PORTDOCS%%share/tinker/test/formbig.key %%PORTDOCS%%share/tinker/test/formbig.xyz +%%PORTDOCS%%share/tinker/test/formbox.dyn %%PORTDOCS%%share/tinker/test/formbox.key %%PORTDOCS%%share/tinker/test/formbox.xyz %%PORTDOCS%%share/tinker/test/furan.int @@ -292,6 +299,7 @@ %%PORTDOCS%%share/tinker/test/hexanes.key %%PORTDOCS%%share/tinker/test/hexanes.run %%PORTDOCS%%share/tinker/test/hexanes.xyz +%%PORTDOCS%%share/tinker/test/hexanex.xyz %%PORTDOCS%%share/tinker/test/imidazole.int %%PORTDOCS%%share/tinker/test/imidazole.key %%PORTDOCS%%share/tinker/test/imidazole.xyz @@ -300,10 +308,14 @@ %%PORTDOCS%%share/tinker/test/imine.xyz %%PORTDOCS%%share/tinker/test/lactam.key %%PORTDOCS%%share/tinker/test/lactam.xyz +%%PORTDOCS%%share/tinker/test/lipid.key +%%PORTDOCS%%share/tinker/test/lipid.xyz %%PORTDOCS%%share/tinker/test/melittin.key %%PORTDOCS%%share/tinker/test/melittin.pdb %%PORTDOCS%%share/tinker/test/melittin.seq %%PORTDOCS%%share/tinker/test/melittin.xyz +%%PORTDOCS%%share/tinker/test/membrane.key +%%PORTDOCS%%share/tinker/test/membrane.xyz %%PORTDOCS%%share/tinker/test/methane.int %%PORTDOCS%%share/tinker/test/methane.key %%PORTDOCS%%share/tinker/test/methane.xyz @@ -314,6 +326,9 @@ %%PORTDOCS%%share/tinker/test/naphthalene.int %%PORTDOCS%%share/tinker/test/naphthalene.key %%PORTDOCS%%share/tinker/test/naphthalene.xyz +%%PORTDOCS%%share/tinker/test/nitrogen.dyn +%%PORTDOCS%%share/tinker/test/nitrogen.key +%%PORTDOCS%%share/tinker/test/nitrogen.xyz %%PORTDOCS%%share/tinker/test/nma.int %%PORTDOCS%%share/tinker/test/nma.key %%PORTDOCS%%share/tinker/test/nma.xyz @@ -342,6 +357,8 @@ %%PORTDOCS%%share/tinker/test/peptide.xyz %%PORTDOCS%%share/tinker/test/phenanth.key %%PORTDOCS%%share/tinker/test/phenanth.xyz +%%PORTDOCS%%share/tinker/test/pol3.key +%%PORTDOCS%%share/tinker/test/pol3.xyz %%PORTDOCS%%share/tinker/test/propane.key %%PORTDOCS%%share/tinker/test/propane.ray %%PORTDOCS%%share/tinker/test/propane.xyz @@ -358,6 +375,8 @@ %%PORTDOCS%%share/tinker/test/pyrrole.xyz %%PORTDOCS%%share/tinker/test/retinoic.key %%PORTDOCS%%share/tinker/test/retinoic.xyz +%%PORTDOCS%%share/tinker/test/skunk.key +%%PORTDOCS%%share/tinker/test/skunk.xyz %%PORTDOCS%%share/tinker/test/sterol.key %%PORTDOCS%%share/tinker/test/sterol.xyz %%PORTDOCS%%share/tinker/test/styrene.int @@ -394,13 +413,16 @@ %%PORTDOCS%%share/tinker/test/watersmall.dyn %%PORTDOCS%%share/tinker/test/watersmall.key %%PORTDOCS%%share/tinker/test/watersmall.xyz +%%PORTDOCS%%share/tinker/test/watertiny.dyn +%%PORTDOCS%%share/tinker/test/watertiny.key +%%PORTDOCS%%share/tinker/test/watertiny.xyz %%PORTDOCS%%share/tinker/test/white.int %%PORTDOCS%%share/tinker/test/white.key %%PORTDOCS%%share/tinker/test/white.xyz -%%PORTDOCS%%share/tinker/tinker.txt +share/tinker/tinker.txt %%PORTDOCS%%@dirrm share/doc/tinker %%PORTDOCS%%@dirrm share/examples/tinker %%PORTDOCS%%@dirrm share/tinker/bench -%%PORTDOCS%%@dirrm share/tinker/params +@dirrm share/tinker/params %%PORTDOCS%%@dirrm share/tinker/test -%%PORTDOCS%%@dirrm share/tinker +@dirrm share/tinker diff -ruN tinker.old/pkg-plist.viewer tinker/pkg-plist.viewer --- tinker.old/pkg-plist.viewer Mon Dec 31 14:45:33 2001 +++ tinker/pkg-plist.viewer Mon Dec 31 21:01:45 2001 @@ -14,6 +14,7 @@ bin/minimize bin/minirot bin/minrigid +bin/monte bin/newton bin/newtrot bin/nucleic @@ -143,20 +144,19 @@ %%PORTDOCS%%share/tinker/bench/results-3.7 %%PORTDOCS%%share/tinker/bench/results-3.8 %%PORTDOCS%%share/tinker/bench/results-3.9 -%%PORTDOCS%%share/tinker/params/README -%%PORTDOCS%%share/tinker/params/amber.prm -%%PORTDOCS%%share/tinker/params/charmm.prm -%%PORTDOCS%%share/tinker/params/dudek.prm -%%PORTDOCS%%share/tinker/params/hoch.prm -%%PORTDOCS%%share/tinker/params/mm2.prm -%%PORTDOCS%%share/tinker/params/mm3.prm -%%PORTDOCS%%share/tinker/params/mm3pro.prm -%%PORTDOCS%%share/tinker/params/opls.prm -%%PORTDOCS%%share/tinker/params/oplsaa.prm -%%PORTDOCS%%share/tinker/params/smooth.prm -%%PORTDOCS%%share/tinker/params/smoothaa.prm -%%PORTDOCS%%share/tinker/params/water.prm -%%PORTDOCS%%share/tinker/rasmol/rasmol.hlp +share/tinker/params/README +share/tinker/params/amber.prm +share/tinker/params/charmm.prm +share/tinker/params/hoch.prm +share/tinker/params/mm2.prm +share/tinker/params/mm3.prm +share/tinker/params/mm3pro.prm +share/tinker/params/opls.prm +share/tinker/params/oplsaa.prm +share/tinker/params/smooth.prm +share/tinker/params/smoothaa.prm +share/tinker/params/water.prm +share/tinker/rasmol/rasmol.hlp %%PORTDOCS%%share/tinker/test/README %%PORTDOCS%%share/tinker/test/ala20.key %%PORTDOCS%%share/tinker/test/ala20.xyz @@ -187,6 +187,9 @@ %%PORTDOCS%%share/tinker/test/bowl2.xyz %%PORTDOCS%%share/tinker/test/bowl3.key %%PORTDOCS%%share/tinker/test/bowl3.xyz +%%PORTDOCS%%share/tinker/test/bucky.int +%%PORTDOCS%%share/tinker/test/bucky.key +%%PORTDOCS%%share/tinker/test/bucky.xyz %%PORTDOCS%%share/tinker/test/butane.int %%PORTDOCS%%share/tinker/test/butane.key %%PORTDOCS%%share/tinker/test/butane.xyz @@ -207,12 +210,12 @@ %%PORTDOCS%%share/tinker/test/c5.key %%PORTDOCS%%share/tinker/test/c5.seq %%PORTDOCS%%share/tinker/test/c5.xyz -%%PORTDOCS%%share/tinker/test/c7ax.key -%%PORTDOCS%%share/tinker/test/c7ax.seq -%%PORTDOCS%%share/tinker/test/c7ax.xyz -%%PORTDOCS%%share/tinker/test/c7eq.key -%%PORTDOCS%%share/tinker/test/c7eq.seq -%%PORTDOCS%%share/tinker/test/c7eq.xyz +%%PORTDOCS%%share/tinker/test/c7a.key +%%PORTDOCS%%share/tinker/test/c7a.seq +%%PORTDOCS%%share/tinker/test/c7a.xyz +%%PORTDOCS%%share/tinker/test/c7e.key +%%PORTDOCS%%share/tinker/test/c7e.seq +%%PORTDOCS%%share/tinker/test/c7e.xyz %%PORTDOCS%%share/tinker/test/calmodulin.key %%PORTDOCS%%share/tinker/test/calmodulin.pdb %%PORTDOCS%%share/tinker/test/calmodulin.seq @@ -250,6 +253,9 @@ %%PORTDOCS%%share/tinker/test/diene.xyz %%PORTDOCS%%share/tinker/test/dimethane.key %%PORTDOCS%%share/tinker/test/dimethane.xyz +%%PORTDOCS%%share/tinker/test/diwater.key +%%PORTDOCS%%share/tinker/test/diwater.lin +%%PORTDOCS%%share/tinker/test/diwater.xyz %%PORTDOCS%%share/tinker/test/enkephalin.int %%PORTDOCS%%share/tinker/test/enkephalin.key %%PORTDOCS%%share/tinker/test/enkephalin.make @@ -276,6 +282,7 @@ %%PORTDOCS%%share/tinker/test/form.xyz %%PORTDOCS%%share/tinker/test/formbig.key %%PORTDOCS%%share/tinker/test/formbig.xyz +%%PORTDOCS%%share/tinker/test/formbox.dyn %%PORTDOCS%%share/tinker/test/formbox.key %%PORTDOCS%%share/tinker/test/formbox.xyz %%PORTDOCS%%share/tinker/test/furan.int @@ -297,6 +304,7 @@ %%PORTDOCS%%share/tinker/test/hexanes.key %%PORTDOCS%%share/tinker/test/hexanes.run %%PORTDOCS%%share/tinker/test/hexanes.xyz +%%PORTDOCS%%share/tinker/test/hexanex.xyz %%PORTDOCS%%share/tinker/test/imidazole.int %%PORTDOCS%%share/tinker/test/imidazole.key %%PORTDOCS%%share/tinker/test/imidazole.xyz @@ -305,10 +313,14 @@ %%PORTDOCS%%share/tinker/test/imine.xyz %%PORTDOCS%%share/tinker/test/lactam.key %%PORTDOCS%%share/tinker/test/lactam.xyz +%%PORTDOCS%%share/tinker/test/lipid.key +%%PORTDOCS%%share/tinker/test/lipid.xyz %%PORTDOCS%%share/tinker/test/melittin.key %%PORTDOCS%%share/tinker/test/melittin.pdb %%PORTDOCS%%share/tinker/test/melittin.seq %%PORTDOCS%%share/tinker/test/melittin.xyz +%%PORTDOCS%%share/tinker/test/membrane.key +%%PORTDOCS%%share/tinker/test/membrane.xyz %%PORTDOCS%%share/tinker/test/methane.int %%PORTDOCS%%share/tinker/test/methane.key %%PORTDOCS%%share/tinker/test/methane.xyz @@ -319,6 +331,9 @@ %%PORTDOCS%%share/tinker/test/naphthalene.int %%PORTDOCS%%share/tinker/test/naphthalene.key %%PORTDOCS%%share/tinker/test/naphthalene.xyz +%%PORTDOCS%%share/tinker/test/nitrogen.dyn +%%PORTDOCS%%share/tinker/test/nitrogen.key +%%PORTDOCS%%share/tinker/test/nitrogen.xyz %%PORTDOCS%%share/tinker/test/nma.int %%PORTDOCS%%share/tinker/test/nma.key %%PORTDOCS%%share/tinker/test/nma.xyz @@ -347,6 +362,8 @@ %%PORTDOCS%%share/tinker/test/peptide.xyz %%PORTDOCS%%share/tinker/test/phenanth.key %%PORTDOCS%%share/tinker/test/phenanth.xyz +%%PORTDOCS%%share/tinker/test/pol3.key +%%PORTDOCS%%share/tinker/test/pol3.xyz %%PORTDOCS%%share/tinker/test/propane.key %%PORTDOCS%%share/tinker/test/propane.ray %%PORTDOCS%%share/tinker/test/propane.xyz @@ -363,6 +380,8 @@ %%PORTDOCS%%share/tinker/test/pyrrole.xyz %%PORTDOCS%%share/tinker/test/retinoic.key %%PORTDOCS%%share/tinker/test/retinoic.xyz +%%PORTDOCS%%share/tinker/test/skunk.key +%%PORTDOCS%%share/tinker/test/skunk.xyz %%PORTDOCS%%share/tinker/test/sterol.key %%PORTDOCS%%share/tinker/test/sterol.xyz %%PORTDOCS%%share/tinker/test/styrene.int @@ -399,14 +418,17 @@ %%PORTDOCS%%share/tinker/test/watersmall.dyn %%PORTDOCS%%share/tinker/test/watersmall.key %%PORTDOCS%%share/tinker/test/watersmall.xyz +%%PORTDOCS%%share/tinker/test/watertiny.dyn +%%PORTDOCS%%share/tinker/test/watertiny.key +%%PORTDOCS%%share/tinker/test/watertiny.xyz %%PORTDOCS%%share/tinker/test/white.int %%PORTDOCS%%share/tinker/test/white.key %%PORTDOCS%%share/tinker/test/white.xyz -%%PORTDOCS%%share/tinker/tinker.txt +share/tinker/tinker.txt %%PORTDOCS%%@dirrm share/doc/tinker %%PORTDOCS%%@dirrm share/examples/tinker %%PORTDOCS%%@dirrm share/tinker/bench -%%PORTDOCS%%@dirrm share/tinker/params -%%PORTDOCS%%@dirrm share/tinker/rasmol +@dirrm share/tinker/params +@dirrm share/tinker/rasmol %%PORTDOCS%%@dirrm share/tinker/test -%%PORTDOCS%%@dirrm share/tinker +@dirrm share/tinker >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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