From c931ed3f31f3276099cb60d3c8edf1f4b13b9307 Mon Sep 17 00:00:00 2001
From: Martin Wilke <miwi@FreeBSD.org>
Date: Mon, 15 Jul 2013 14:50:22 +0000
Subject: [PATCH] - Update to 6.2.06

PR:		180518
Submitted by:	Ports Fury
---
 biology/tinker/Makefile                   |  5 ++++-
 biology/tinker/distinfo                   |  4 ++--
 biology/tinker/files/patch-make__Makefile | 24 ++++++++++++++---------
 biology/tinker/pkg-plist                  |  3 ++-
 4 files changed, 23 insertions(+), 13 deletions(-)

diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index 3db597fbf307..64f4665c533d 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -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})
diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo
index 9d2a2c3ec6bb..f0a7613dac6f 100644
--- a/biology/tinker/distinfo
+++ b/biology/tinker/distinfo
@@ -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 --git a/biology/tinker/files/patch-make__Makefile b/biology/tinker/files/patch-make__Makefile
index 3b7c2090ad5d..0fa8c9e795c2 100644
--- a/biology/tinker/files/patch-make__Makefile
+++ b/biology/tinker/files/patch-make__Makefile
@@ -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 --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index 8e28b77a4292..2a034a061e4f 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -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