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Message-Id: <20130713025841.27c5f1b583f171db59d8dcbd@yahoo.com>
Date: Sat, 13 Jul 2013 02:58:41 +0900
From: KATO Tsuguru <tkato432@yahoo.com>
To: FreeBSD-gnats-submit@FreeBSD.org
Subject: biology/tinker: Update to version 6.2.06

>Number:         180518
>Category:       ports
>Synopsis:       biology/tinker: Update to version 6.2.06
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    miwi
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Fri Jul 12 18:10:06 UTC 2013
>Closed-Date:    Mon Jul 15 14:50:30 UTC 2013
>Last-Modified:  Mon Jul 15 15:00:04 UTC 2013
>Originator:     KATO Tsuguru
>Release:        FreeBSD 8.4-RELEASE i386
>Organization:
>Environment:
>Description:
- Update to version 6.2.06

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/tinker/Makefile biology/tinker/Makefile
--- /usr/ports/biology/tinker/Makefile	2013-06-21 03:53:38.000000000 +0900
+++ biology/tinker/Makefile	2013-07-13 00:00:00.000000000 +0900
@@ -2,7 +2,7 @@
 # $FreeBSD: head/biology/tinker/Makefile 319343 2013-05-29 05:25:49Z miwi $
 
 PORTNAME=	tinker
-PORTVERSION=	6.2.05
+PORTVERSION=	6.2.06
 CATEGORIES=	biology
 MASTER_SITES=	http://dasher.wustl.edu/tinker/downloads/
 
@@ -39,6 +39,9 @@
 post-extract:
 	@${CHMOD} -R u+w ${WRKSRC}
 
+pre-build:
+	@${RM} -f ${BUILD_WRKSRC}/*.c 
+
 post-install:
 	@${MKDIR} ${DATADIR}
 	(cd ${INSTALL_WRKSRC} && ${INSTALL_DATA} tinker.txt ${DATADIR})
diff -urN /usr/ports/biology/tinker/distinfo biology/tinker/distinfo
--- /usr/ports/biology/tinker/distinfo	2013-06-21 03:53:38.000000000 +0900
+++ biology/tinker/distinfo	2013-07-13 00:00:00.000000000 +0900
@@ -1,2 +1,2 @@
-SHA256 (tinker-6.2.05.tar.gz) = 73dcb0fff809bd38e8fbede896b778302ff1e89c90129ca30b54d773b2ea8e50
-SIZE (tinker-6.2.05.tar.gz) = 20246464
+SHA256 (tinker-6.2.06.tar.gz) = 6d5e79cd2a431787cd77bce2c469b7eec219f8e874425dcf8ebb74dabb0d985c
+SIZE (tinker-6.2.06.tar.gz) = 20182802
diff -urN /usr/ports/biology/tinker/files/patch-make__Makefile biology/tinker/files/patch-make__Makefile
--- /usr/ports/biology/tinker/files/patch-make__Makefile	2013-06-21 03:53:38.000000000 +0900
+++ biology/tinker/files/patch-make__Makefile	2013-07-13 00:00:00.000000000 +0900
@@ -53,18 +53,18 @@
  
  ##
  ##  Machine:  Macintosh
-@@ -595,6 +609,8 @@
+@@ -597,14 +611,13 @@
             xyzpdb.x \
             xyzsybyl.x
  
+-%.o: %.f
+-	${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ 
 +.SUFFIXES: .x
-+
- .f.o:
- 	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f 
- 
-@@ -604,8 +620,8 @@
- server.o:
- 	${F77} ${F77FLAGS} ${OPTFLAGS} server.f
+ 
+-%.o: %.c
+-	${CC} ${CFLAGS} ${INCLUDEDIR} ${OPTFLAGS} $<
++.f.o:
++	${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ 
  
 -%.x: %.o libtinker.a
 -	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
@@ -73,14 +73,19 @@
  
  all:	${EXEFILES}
  
-@@ -616,66 +632,66 @@
- 	cat *.i *.f *.c > tinker.txt
+@@ -612,70 +625,70 @@
+ 	rm -f *.o *.a *.x
+ 
+ listing:
+-	cat *.i *.f *.c > tinker.txt
++	cat *.i *.f > tinker.txt
  
  rename:
 -	mv  alchemy.x    $(BINDIR)/alchemy
 -	mv  analyze.x    $(BINDIR)/analyze
 -	mv  anneal.x     $(BINDIR)/anneal
 -	mv  archive.x    $(BINDIR)/archive
+-	mv  bar.x        $(BINDIR)/bar
 -	mv  correlate.x  $(BINDIR)/correlate
 -	mv  crystal.x    $(BINDIR)/crystal
 -	mv  diffuse.x    $(BINDIR)/diffuse
@@ -141,6 +146,7 @@
 +	${BSD_INSTALL_PROGRAM}  analyze.x    $(BINDIR)/analyze
 +	${BSD_INSTALL_PROGRAM}  anneal.x     $(BINDIR)/anneal
 +	${BSD_INSTALL_PROGRAM}  archive.x    $(BINDIR)/archive
++	${BSD_INSTALL_PROGRAM}  bar.x        $(BINDIR)/bar
 +	${BSD_INSTALL_PROGRAM}  correlate.x  $(BINDIR)/correlate
 +	${BSD_INSTALL_PROGRAM}  crystal.x    $(BINDIR)/crystal
 +	${BSD_INSTALL_PROGRAM}  diffuse.x    $(BINDIR)/diffuse
diff -urN /usr/ports/biology/tinker/pkg-plist biology/tinker/pkg-plist
--- /usr/ports/biology/tinker/pkg-plist	2013-06-21 03:53:38.000000000 +0900
+++ biology/tinker/pkg-plist	2013-07-13 00:00:00.000000000 +0900
@@ -2,6 +2,7 @@
 bin/analyze
 bin/anneal
 bin/archive
+bin/bar
 bin/correlate
 bin/crystal
 bin/diffuse
@@ -156,6 +157,7 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.xyz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.key
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.dyn
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.key
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.pdb
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.seq
@@ -279,7 +281,6 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.xyz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/membrane.key
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/membrane.xyz
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.dyn
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.key
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.xyz
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane.int
>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->miwi 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Fri Jul 12 18:11:50 UTC 2013 
Responsible-Changed-Why:  
miwi@ wants this submitter's PRs (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=180518 
State-Changed-From-To: open->closed 
State-Changed-By: miwi 
State-Changed-When: Mon Jul 15 14:50:30 UTC 2013 
State-Changed-Why:  
Committed. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=180518 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/180518: commit references a PR
Date: Mon, 15 Jul 2013 14:50:32 +0000 (UTC)

 Author: miwi
 Date: Mon Jul 15 14:50:22 2013
 New Revision: 323046
 URL: http://svnweb.freebsd.org/changeset/ports/323046
 
 Log:
   - Update to 6.2.06
   
   PR:		180518
   Submitted by:	Ports Fury
 
 Modified:
   head/biology/tinker/Makefile
   head/biology/tinker/distinfo
   head/biology/tinker/files/patch-make__Makefile
   head/biology/tinker/pkg-plist
 
 Modified: head/biology/tinker/Makefile
 ==============================================================================
 --- head/biology/tinker/Makefile	Mon Jul 15 14:49:39 2013	(r323045)
 +++ head/biology/tinker/Makefile	Mon Jul 15 14:50:22 2013	(r323046)
 @@ -2,7 +2,7 @@
  # $FreeBSD$
  
  PORTNAME=	tinker
 -PORTVERSION=	6.2.05
 +PORTVERSION=	6.2.06
  CATEGORIES=	biology
  MASTER_SITES=	http://dasher.wustl.edu/tinker/downloads/
  
 @@ -39,6 +39,9 @@ FFLAGS+=	-mfancy-math-387 -malign-double
  post-extract:
  	@${CHMOD} -R u+w ${WRKSRC}
  
 +pre-build:
 +	@${RM} -f ${BUILD_WRKSRC}/*.c 
 +
  post-install:
  	@${MKDIR} ${DATADIR}
  	(cd ${INSTALL_WRKSRC} && ${INSTALL_DATA} tinker.txt ${DATADIR})
 
 Modified: head/biology/tinker/distinfo
 ==============================================================================
 --- head/biology/tinker/distinfo	Mon Jul 15 14:49:39 2013	(r323045)
 +++ head/biology/tinker/distinfo	Mon Jul 15 14:50:22 2013	(r323046)
 @@ -1,2 +1,2 @@
 -SHA256 (tinker-6.2.05.tar.gz) = 73dcb0fff809bd38e8fbede896b778302ff1e89c90129ca30b54d773b2ea8e50
 -SIZE (tinker-6.2.05.tar.gz) = 20246464
 +SHA256 (tinker-6.2.06.tar.gz) = 6d5e79cd2a431787cd77bce2c469b7eec219f8e874425dcf8ebb74dabb0d985c
 +SIZE (tinker-6.2.06.tar.gz) = 20182802
 
 Modified: head/biology/tinker/files/patch-make__Makefile
 ==============================================================================
 --- head/biology/tinker/files/patch-make__Makefile	Mon Jul 15 14:49:39 2013	(r323045)
 +++ head/biology/tinker/files/patch-make__Makefile	Mon Jul 15 14:50:22 2013	(r323046)
 @@ -53,18 +53,18 @@
   
   ##
   ##  Machine:  Macintosh
 -@@ -595,6 +609,8 @@
 +@@ -597,14 +611,13 @@
              xyzpdb.x \
              xyzsybyl.x
   
 +-%.o: %.f
 +-	${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ 
  +.SUFFIXES: .x
 -+
 - .f.o:
 - 	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f 
 - 
 -@@ -604,8 +620,8 @@
 - server.o:
 - 	${F77} ${F77FLAGS} ${OPTFLAGS} server.f
 + 
 +-%.o: %.c
 +-	${CC} ${CFLAGS} ${INCLUDEDIR} ${OPTFLAGS} $<
 ++.f.o:
 ++	${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ 
   
  -%.x: %.o libtinker.a
  -	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
 @@ -73,14 +73,19 @@
   
   all:	${EXEFILES}
   
 -@@ -616,66 +632,66 @@
 - 	cat *.i *.f *.c > tinker.txt
 +@@ -612,70 +625,70 @@
 + 	rm -f *.o *.a *.x
 + 
 + listing:
 +-	cat *.i *.f *.c > tinker.txt
 ++	cat *.i *.f > tinker.txt
   
   rename:
  -	mv  alchemy.x    $(BINDIR)/alchemy
  -	mv  analyze.x    $(BINDIR)/analyze
  -	mv  anneal.x     $(BINDIR)/anneal
  -	mv  archive.x    $(BINDIR)/archive
 +-	mv  bar.x        $(BINDIR)/bar
  -	mv  correlate.x  $(BINDIR)/correlate
  -	mv  crystal.x    $(BINDIR)/crystal
  -	mv  diffuse.x    $(BINDIR)/diffuse
 @@ -141,6 +146,7 @@
  +	${BSD_INSTALL_PROGRAM}  analyze.x    $(BINDIR)/analyze
  +	${BSD_INSTALL_PROGRAM}  anneal.x     $(BINDIR)/anneal
  +	${BSD_INSTALL_PROGRAM}  archive.x    $(BINDIR)/archive
 ++	${BSD_INSTALL_PROGRAM}  bar.x        $(BINDIR)/bar
  +	${BSD_INSTALL_PROGRAM}  correlate.x  $(BINDIR)/correlate
  +	${BSD_INSTALL_PROGRAM}  crystal.x    $(BINDIR)/crystal
  +	${BSD_INSTALL_PROGRAM}  diffuse.x    $(BINDIR)/diffuse
 
 Modified: head/biology/tinker/pkg-plist
 ==============================================================================
 --- head/biology/tinker/pkg-plist	Mon Jul 15 14:49:39 2013	(r323045)
 +++ head/biology/tinker/pkg-plist	Mon Jul 15 14:50:22 2013	(r323046)
 @@ -2,6 +2,7 @@ bin/alchemy
  bin/analyze
  bin/anneal
  bin/archive
 +bin/bar
  bin/correlate
  bin/crystal
  bin/diffuse
 @@ -156,6 +157,7 @@ bin/xyzsybyl
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.xyz
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.key
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.xyz
 +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.dyn
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.key
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.pdb
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.seq
 @@ -279,7 +281,6 @@ bin/xyzsybyl
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.xyz
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/membrane.key
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/membrane.xyz
 -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.dyn
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.key
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.xyz
  %%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane.int
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