Date: Tue, 20 May 2003 16:27:29 -0500 (CDT) From: Glenn Johnson <gjohnson@srrc.ars.usda.gov> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/52498: Maintainer update of biology/tinker port Message-ID: <200305202127.h4KLRTTs046825@node1.cluster.srrc.usda.gov> Resent-Message-ID: <200305202130.h4KLU58O018442@freefall.freebsd.org>
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>Number: 52498
>Category: ports
>Synopsis: Maintainer update of biology/tinker port
>Confidential: no
>Severity: serious
>Priority: medium
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Tue May 20 14:30:05 PDT 2003
>Closed-Date:
>Last-Modified:
>Originator: Glenn Johnson
>Release: FreeBSD 5.1-BETA i386
>Organization:
>Environment:
System: FreeBSD node1.cluster.srrc.usda.gov 5.1-BETA FreeBSD 5.1-BETA #0: Tue May 20 14:08:40 CDT 2003 root@node1.cluster.srrc.usda.gov:/usr/obj/usr/src/sys/CLUSTER-FW i386
>Description:
Maintainer update of biology/tinker port to version 4.0.
>How-To-Repeat:
<code/input/activities to reproduce the problem (multiple
lines)>
>Fix:
Note that $PORTSDIR/biology/tinker/files/patch-openend.f is a
new file.
--- tinker-update begins here ---
diff -ruN biology/tinker.orig/Makefile biology/tinker/Makefile
--- biology/tinker.orig/Makefile Mon May 12 17:17:28 2003
+++ biology/tinker/Makefile Tue May 20 15:33:44 2003
@@ -6,8 +6,7 @@
#
PORTNAME= tinker
-PORTVERSION= 3.9
-PORTREVISION= 1
+PORTVERSION= 4.0
CATEGORIES= biology
MASTER_SITES= ftp://dasher.wustl.edu/pub/
DISTNAME= ${PORTNAME}
@@ -24,11 +23,6 @@
INSTALL_TARGET= rename
RESTRICTED= author requests no distribution except from his FTP site
-
-pre-fetch:
- @${ECHO_MSG} ""
- @${ECHO_MSG} If you get a CHECKSUM mismatch, try doing a \'make distclean\' first.
- @${ECHO_MSG} ""
.include <bsd.port.pre.mk>
diff -ruN biology/tinker.orig/distinfo biology/tinker/distinfo
--- biology/tinker.orig/distinfo Mon May 12 17:17:28 2003
+++ biology/tinker/distinfo Tue May 20 13:35:42 2003
@@ -1 +1 @@
-MD5 (tinker.tar.gz) = e6f34c61cc40f107fbbcf4b0c7dae5a5
+MD5 (tinker.tar.gz) = 571224cc0de71099b59de74b3dca648d
diff -ruN biology/tinker.orig/files/patch-aa biology/tinker/files/patch-aa
--- biology/tinker.orig/files/patch-aa Mon May 12 17:17:28 2003
+++ biology/tinker/files/patch-aa Tue May 20 13:53:53 2003
@@ -1,5 +1,8 @@
---- ../make/Makefile.orig Tue Nov 13 10:16:27 2001
-+++ ../make/Makefile Mon Dec 31 15:33:40 2001
+
+$FreeBSD$
+
+--- ../make/Makefile.orig Fri Apr 18 13:32:36 2003
++++ ../make/Makefile Tue May 20 13:48:01 2003
@@ -9,8 +9,8 @@
##
## 1. make all Build all the TINKER executables
@@ -24,26 +27,26 @@
####################################################################
## Known Machine Types; Uncomment One of the Following Sections ##
-@@ -87,12 +87,12 @@
- ## Compiler: GNU g77
+@@ -101,12 +101,12 @@
+ ## Compiler: Intel Fortran
##
--F77 = /usr/bin/g77
+-F77 = /usr/intel/compiler70/ia32/bin/ifc
-LIBS =
-F77FLAGS = -c
--OPTFLAGS = -O3 -ffast-math
+-OPTFLAGS = -O2 -cm -w
-LIBFLAGS = -crusv
--LINKFLAGS =
-+#F77 = /usr/bin/g77
+-LINKFLAGS = -Vaxlib
++#F77 = /usr/intel/compiler70/ia32/bin/ifc
+#LIBS =
+#F77FLAGS = -c
-+#OPTFLAGS = -O3 -ffast-math
++#OPTFLAGS = -O2 -cm -w
+#LIBFLAGS = -crusv
-+#LINKFLAGS =
++#LINKFLAGS = -Vaxlib
##
## Machine: IntelPC / Linux
-@@ -108,6 +108,24 @@
+@@ -122,6 +122,24 @@
#LIBFLAGS = -crusv
#LINKFLAGS =
@@ -68,7 +71,7 @@
#################################################################
## Should not be Necessary to Change Things Below this Point ##
#################################################################
-@@ -497,11 +515,13 @@
+@@ -522,11 +540,13 @@
xyzpdb.x \
xyzsybyl.x
@@ -84,7 +87,7 @@
all: ${EXEFILES}
-@@ -512,58 +532,58 @@
+@@ -537,58 +557,58 @@
cat *.i *.f > tinker.txt
rename:
diff -ruN biology/tinker.orig/files/patch-openend.f biology/tinker/files/patch-openend.f
--- biology/tinker.orig/files/patch-openend.f Wed Dec 31 18:00:00 1969
+++ biology/tinker/files/patch-openend.f Tue May 20 14:30:20 2003
@@ -0,0 +1,19 @@
+
+$FreeBSD$
+
+--- openend.f.orig Tue May 20 14:29:37 2003
++++ openend.f Tue May 20 14:29:50 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
diff -ruN biology/tinker.orig/pkg-plist biology/tinker/pkg-plist
--- biology/tinker.orig/pkg-plist Mon May 12 17:17:28 2003
+++ biology/tinker/pkg-plist Tue May 20 15:28:55 2003
@@ -57,6 +57,8 @@
%%PORTDOCS%%share/doc/tinker/license.pdf
%%PORTDOCS%%share/doc/tinker/license.ps
%%PORTDOCS%%share/doc/tinker/license.txt
+%%PORTDOCS%%share/doc/tinker/logo-bind.pdf
+%%PORTDOCS%%share/doc/tinker/logo-bind.ps.gz
%%PORTDOCS%%share/doc/tinker/logo.pdf
%%PORTDOCS%%share/doc/tinker/logo.ps.gz
%%PORTDOCS%%share/doc/tinker/release-3.2
@@ -64,6 +66,7 @@
%%PORTDOCS%%share/doc/tinker/release-3.7
%%PORTDOCS%%share/doc/tinker/release-3.8
%%PORTDOCS%%share/doc/tinker/release-3.9
+%%PORTDOCS%%share/doc/tinker/release-4.0
%%PORTDOCS%%share/doc/tinker/summary.pdf
%%PORTDOCS%%share/doc/tinker/summary.ps
%%PORTDOCS%%share/doc/tinker/summary.txt
@@ -140,15 +143,21 @@
%%PORTDOCS%%share/tinker/bench/results-3.7
%%PORTDOCS%%share/tinker/bench/results-3.8
%%PORTDOCS%%share/tinker/bench/results-3.9
+%%PORTDOCS%%share/tinker/bench/results-4.0
share/tinker/params/README
-share/tinker/params/amber.prm
-share/tinker/params/charmm.prm
+share/tinker/params/amber94.prm
+share/tinker/params/amber96.prm
+share/tinker/params/amber98.prm
+share/tinker/params/amoeba.prm
+share/tinker/params/charmm19.prm
+share/tinker/params/charmm27.prm
+share/tinker/params/dudek.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/oplsua.prm
share/tinker/params/smooth.prm
share/tinker/params/smoothaa.prm
share/tinker/params/water.prm
@@ -157,6 +166,8 @@
%%PORTDOCS%%share/tinker/test/ala20.xyz
%%PORTDOCS%%share/tinker/test/alkane.key
%%PORTDOCS%%share/tinker/test/alkane.xyz
+%%PORTDOCS%%share/tinker/test/amoeba.key
+%%PORTDOCS%%share/tinker/test/amoeba.xyz
%%PORTDOCS%%share/tinker/test/arach.int
%%PORTDOCS%%share/tinker/test/arach.key
%%PORTDOCS%%share/tinker/test/arach.xyz
@@ -222,7 +233,6 @@
%%PORTDOCS%%share/tinker/test/crambin.key
%%PORTDOCS%%share/tinker/test/crambin.pdb
%%PORTDOCS%%share/tinker/test/crambin.seq
-%%PORTDOCS%%share/tinker/test/crambin.super
%%PORTDOCS%%share/tinker/test/crambin.xyz
%%PORTDOCS%%share/tinker/test/crambinx.key
%%PORTDOCS%%share/tinker/test/crambinx.ray
@@ -248,9 +258,6 @@
%%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
@@ -285,6 +292,9 @@
%%PORTDOCS%%share/tinker/test/furan.xyz
%%PORTDOCS%%share/tinker/test/glucose.key
%%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/glycerol.dyn
+%%PORTDOCS%%share/tinker/test/glycerol.key
+%%PORTDOCS%%share/tinker/test/glycerol.xyz
%%PORTDOCS%%share/tinker/test/graphite.key
%%PORTDOCS%%share/tinker/test/graphite.xyz
%%PORTDOCS%%share/tinker/test/helix.dyn
@@ -299,7 +309,6 @@
%%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
@@ -357,6 +366,10 @@
%%PORTDOCS%%share/tinker/test/peptide.xyz
%%PORTDOCS%%share/tinker/test/phenanth.key
%%PORTDOCS%%share/tinker/test/phenanth.xyz
+%%PORTDOCS%%share/tinker/test/photo.key
+%%PORTDOCS%%share/tinker/test/photo.pdb
+%%PORTDOCS%%share/tinker/test/photo.seq
+%%PORTDOCS%%share/tinker/test/photo.xyz
%%PORTDOCS%%share/tinker/test/pol3.key
%%PORTDOCS%%share/tinker/test/pol3.xyz
%%PORTDOCS%%share/tinker/test/propane.key
@@ -397,6 +410,10 @@
%%PORTDOCS%%share/tinker/test/tip4p.xyz
%%PORTDOCS%%share/tinker/test/tip5p.key
%%PORTDOCS%%share/tinker/test/tip5p.xyz
+%%PORTDOCS%%share/tinker/test/trpcage.key
+%%PORTDOCS%%share/tinker/test/trpcage.pdb
+%%PORTDOCS%%share/tinker/test/trpcage.seq
+%%PORTDOCS%%share/tinker/test/trpcage.xyz
%%PORTDOCS%%share/tinker/test/water.int
%%PORTDOCS%%share/tinker/test/water.key
%%PORTDOCS%%share/tinker/test/water.xyz
diff -ruN biology/tinker.orig/pkg-plist.viewer biology/tinker/pkg-plist.viewer
--- biology/tinker.orig/pkg-plist.viewer Mon May 12 17:17:28 2003
+++ biology/tinker/pkg-plist.viewer Tue May 20 15:28:40 2003
@@ -61,6 +61,8 @@
%%PORTDOCS%%share/doc/tinker/license.pdf
%%PORTDOCS%%share/doc/tinker/license.ps
%%PORTDOCS%%share/doc/tinker/license.txt
+%%PORTDOCS%%share/doc/tinker/logo-bind.pdf
+%%PORTDOCS%%share/doc/tinker/logo-bind.ps.gz
%%PORTDOCS%%share/doc/tinker/logo.pdf
%%PORTDOCS%%share/doc/tinker/logo.ps.gz
%%PORTDOCS%%share/doc/tinker/release-3.2
@@ -68,6 +70,7 @@
%%PORTDOCS%%share/doc/tinker/release-3.7
%%PORTDOCS%%share/doc/tinker/release-3.8
%%PORTDOCS%%share/doc/tinker/release-3.9
+%%PORTDOCS%%share/doc/tinker/release-4.0
%%PORTDOCS%%share/doc/tinker/summary.pdf
%%PORTDOCS%%share/doc/tinker/summary.ps
%%PORTDOCS%%share/doc/tinker/summary.txt
@@ -144,15 +147,21 @@
%%PORTDOCS%%share/tinker/bench/results-3.7
%%PORTDOCS%%share/tinker/bench/results-3.8
%%PORTDOCS%%share/tinker/bench/results-3.9
+%%PORTDOCS%%share/tinker/bench/results-4.0
share/tinker/params/README
-share/tinker/params/amber.prm
-share/tinker/params/charmm.prm
+share/tinker/params/amber94.prm
+share/tinker/params/amber96.prm
+share/tinker/params/amber98.prm
+share/tinker/params/amoeba.prm
+share/tinker/params/charmm19.prm
+share/tinker/params/charmm27.prm
+share/tinker/params/dudek.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/oplsua.prm
share/tinker/params/smooth.prm
share/tinker/params/smoothaa.prm
share/tinker/params/water.prm
@@ -162,6 +171,8 @@
%%PORTDOCS%%share/tinker/test/ala20.xyz
%%PORTDOCS%%share/tinker/test/alkane.key
%%PORTDOCS%%share/tinker/test/alkane.xyz
+%%PORTDOCS%%share/tinker/test/amoeba.key
+%%PORTDOCS%%share/tinker/test/amoeba.xyz
%%PORTDOCS%%share/tinker/test/arach.int
%%PORTDOCS%%share/tinker/test/arach.key
%%PORTDOCS%%share/tinker/test/arach.xyz
@@ -227,7 +238,6 @@
%%PORTDOCS%%share/tinker/test/crambin.key
%%PORTDOCS%%share/tinker/test/crambin.pdb
%%PORTDOCS%%share/tinker/test/crambin.seq
-%%PORTDOCS%%share/tinker/test/crambin.super
%%PORTDOCS%%share/tinker/test/crambin.xyz
%%PORTDOCS%%share/tinker/test/crambinx.key
%%PORTDOCS%%share/tinker/test/crambinx.ray
@@ -253,9 +263,6 @@
%%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
@@ -290,6 +297,9 @@
%%PORTDOCS%%share/tinker/test/furan.xyz
%%PORTDOCS%%share/tinker/test/glucose.key
%%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/glycerol.dyn
+%%PORTDOCS%%share/tinker/test/glycerol.key
+%%PORTDOCS%%share/tinker/test/glycerol.xyz
%%PORTDOCS%%share/tinker/test/graphite.key
%%PORTDOCS%%share/tinker/test/graphite.xyz
%%PORTDOCS%%share/tinker/test/helix.dyn
@@ -304,7 +314,6 @@
%%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
@@ -362,6 +371,10 @@
%%PORTDOCS%%share/tinker/test/peptide.xyz
%%PORTDOCS%%share/tinker/test/phenanth.key
%%PORTDOCS%%share/tinker/test/phenanth.xyz
+%%PORTDOCS%%share/tinker/test/photo.key
+%%PORTDOCS%%share/tinker/test/photo.pdb
+%%PORTDOCS%%share/tinker/test/photo.seq
+%%PORTDOCS%%share/tinker/test/photo.xyz
%%PORTDOCS%%share/tinker/test/pol3.key
%%PORTDOCS%%share/tinker/test/pol3.xyz
%%PORTDOCS%%share/tinker/test/propane.key
@@ -402,6 +415,10 @@
%%PORTDOCS%%share/tinker/test/tip4p.xyz
%%PORTDOCS%%share/tinker/test/tip5p.key
%%PORTDOCS%%share/tinker/test/tip5p.xyz
+%%PORTDOCS%%share/tinker/test/trpcage.key
+%%PORTDOCS%%share/tinker/test/trpcage.pdb
+%%PORTDOCS%%share/tinker/test/trpcage.seq
+%%PORTDOCS%%share/tinker/test/trpcage.xyz
%%PORTDOCS%%share/tinker/test/water.int
%%PORTDOCS%%share/tinker/test/water.key
%%PORTDOCS%%share/tinker/test/water.xyz
@@ -428,7 +445,7 @@
%%PORTDOCS%%@dirrm share/doc/tinker
%%PORTDOCS%%@dirrm share/examples/tinker
%%PORTDOCS%%@dirrm share/tinker/bench
-@dirrm share/tinker/params
@dirrm share/tinker/rasmol
+@dirrm share/tinker/params
%%PORTDOCS%%@dirrm share/tinker/test
@dirrm share/tinker
--- tinker-update ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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