From 908f72ff107dea687ffd3bee46bb00028f34cdac Mon Sep 17 00:00:00 2001
From: Muhammad Moinur Rahman <bofh@FreeBSD.org>
Date: Sun, 5 Dec 2021 16:44:15 -0600
Subject: [PATCH] biology/seaview: Update version 5.0.4=>5.0.5

Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES
---
 biology/seaview/Makefile                   |  5 +-
 biology/seaview/distinfo                   |  6 +-
 biology/seaview/files/patch-csrc_dnapars.c | 70 ----------------------
 3 files changed, 4 insertions(+), 77 deletions(-)
 delete mode 100644 biology/seaview/files/patch-csrc_dnapars.c

diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile
index 3508d87dfddc..f36b20cc0ccf 100644
--- a/biology/seaview/Makefile
+++ b/biology/seaview/Makefile
@@ -1,7 +1,7 @@
 # Created by: frankch@waru.life.nthu.edu.tw
 
 PORTNAME=	seaview
-PORTVERSION=	5.0.4
+PORTVERSION=	5.0.5
 PORTEPOCH=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
@@ -37,9 +37,6 @@ post-patch:
 	${REINPLACE_CMD} -e \
 		's|^\(CC\) |#\1 | ; s|-ldl || ; \
 		s|^\(CXX\) |#\1 |' ${WRKSRC}/Makefile
-	${REINPLACE_CMD} -E \
-		'/firstplotblock|javarun|\*progname/s,^,extern ,' \
-		${WRKSRC}/csrc/phylip.h ${WRKSRC}/csrc/protpars.c
 	${ECHO_CMD} 'boolean javarun;' >> ${WRKSRC}/csrc/phylip.c
 
 do-install:
diff --git a/biology/seaview/distinfo b/biology/seaview/distinfo
index 808ce3214db5..7afee1b07658 100644
--- a/biology/seaview/distinfo
+++ b/biology/seaview/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1592674569
-SHA256 (seaview_5.0.4.tar.gz) = e153e7fe1dd0b466ce7a00e8b78d5d232aa26063ab82f78eb43811780c41d727
-SIZE (seaview_5.0.4.tar.gz) = 472837
+TIMESTAMP = 1638663734
+SHA256 (seaview_5.0.5.tar.gz) = ce8f5e98ba47883bfa91e91bc79e4d3a26f158dd9983b5e78331a452a4b1f8f2
+SIZE (seaview_5.0.5.tar.gz) = 471739
diff --git a/biology/seaview/files/patch-csrc_dnapars.c b/biology/seaview/files/patch-csrc_dnapars.c
deleted file mode 100644
index ecf81d66f4ae..000000000000
--- a/biology/seaview/files/patch-csrc_dnapars.c
+++ /dev/null
@@ -1,70 +0,0 @@
---- csrc/dnapars.c.orig	2019-11-29 14:00:33 UTC
-+++ csrc/dnapars.c
-@@ -77,41 +77,44 @@ void   load_tree(long treei);
- /* function prototypes */
- 
- 
--Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
-+extern Char infilename[FNMLNGTH], outfilename[FNMLNGTH], intreename[FNMLNGTH], *outtreename,
-      weightfilename[FNMLNGTH];
- char basechar[32]="ACMGRSVTWYHKDBNO???????????????";
--node *root;
--long chars, col, msets, ith, njumble, jumb, maxtrees;
-+extern node *root;
-+extern long chars, col, msets, ith, njumble, jumb;
-+long maxtrees;
- /*   chars = number of sites in actual sequences */
--long inseed, inseed0;
--double threshold;
--boolean jumble, usertree, thresh, weights, thorough, rearrfirst,
--          trout, progress, stepbox, ancseq, mulsets, justwts, firstset, mulf,
--          multf;
-+extern long inseed, inseed0;
-+extern double threshold;
-+extern boolean jumble, usertree, thresh, weights,
-+          trout, progress, stepbox, ancseq, mulsets, justwts, firstset;
-+boolean thorough, rearrfirst, mulf, multf;
- steptr oldweight;
--longer seed;
--pointarray treenode;            /* pointers to all nodes in tree */
--long *enterorder;
-+extern longer seed;
-+extern pointarray treenode;            /* pointers to all nodes in tree */
-+extern long *enterorder;
- long *zeros;
- 
- /* local variables for Pascal maketree, propagated globally for C version: */
- 
--long minwhich;
-+extern long minwhich;
- static double like, minsteps, bestyet, bestlike, bstlike2;
--boolean lastrearr, recompute;
--double nsteps[maxuser];
--long **fsteps;
--node *there, *oldnufork;
--long *place;
--bestelm *bestrees;
--long *threshwt;
-+extern boolean lastrearr, recompute;
-+extern double nsteps[maxuser];
-+extern long **fsteps;
-+extern node *there;
-+node *oldnufork;
-+extern long *place;
-+extern bestelm *bestrees;
-+extern long *threshwt;
- baseptr nothing;
--gbases *garbage;
--node *temp, *temp1, *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
-+extern gbases *garbage;
-+extern node *temp, *temp1;
-+node *temp2, *tempsum, *temprm, *tempadd, *tempf, *tmp, *tmp1,
-        *tmp2, *tmp3, *tmprm, *tmpadd;
--boolean *names;
-+extern boolean *names;
- node *grbg;
--char *progname;
-+extern char *progname;
- 
- 
- static void getoptions(int arg_maxtrees, dnapars_S_option s_option)