From 047a903a15dd3c02ebcda13abd0e5869639bd8b9 Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Fri, 10 May 2019 21:04:43 +0000
Subject: [PATCH] biology/stacks: Upgrade to 2.4

Improve check to avoid outdated GCC on 2nd tier platforms

Reported by:    portscout
---
 biology/stacks/Makefile  |  5 +++--
 biology/stacks/distinfo  |  6 ++---
 biology/stacks/pkg-plist | 47 ----------------------------------------
 3 files changed, 6 insertions(+), 52 deletions(-)

diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile
index d7e0d0938118..f2e69b114170 100644
--- a/biology/stacks/Makefile
+++ b/biology/stacks/Makefile
@@ -1,7 +1,7 @@
 # $FreeBSD$
 
 PORTNAME=	stacks
-DISTVERSION=	2.3
+DISTVERSION=	2.4
 CATEGORIES=	biology perl5 python
 MASTER_SITES=	http://catchenlab.life.illinois.edu/stacks/source/
 
@@ -21,7 +21,8 @@ LDFLAGS+=	-lpthread
 
 .include <bsd.port.pre.mk>
 
-.if ${ARCH} != amd64 && ${ARCH} != i386
+# Force newer GCC on platforms using GCC 4.2 as base
+.if ${CHOSEN_COMPILER_TYPE} == gcc
 USE_GCC=	yes
 .endif
 
diff --git a/biology/stacks/distinfo b/biology/stacks/distinfo
index d8c244d985e0..312ef425ec9d 100644
--- a/biology/stacks/distinfo
+++ b/biology/stacks/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1547306940
-SHA256 (stacks-2.3.tar.gz) = 2a5befaf11ca2f191afcd42a3a3392290d6a116d7fe737b69a2c4d5b77f40c99
-SIZE (stacks-2.3.tar.gz) = 10962586
+TIMESTAMP = 1557519159
+SHA256 (stacks-2.4.tar.gz) = 30093d688a2dc62a19ea42a58065f024c8279419439049bcde186703e75641c1
+SIZE (stacks-2.4.tar.gz) = 10930616
diff --git a/biology/stacks/pkg-plist b/biology/stacks/pkg-plist
index 6660e468dce5..605cf4a295db 100644
--- a/biology/stacks/pkg-plist
+++ b/biology/stacks/pkg-plist
@@ -16,50 +16,3 @@ bin/stacks-gdb
 bin/stacks-integrate-alignments
 bin/tsv2bam
 bin/ustacks
-%%DATADIR%%/php/CatalogClass.php
-%%DATADIR%%/php/Locus.php
-%%DATADIR%%/php/ajax.js
-%%DATADIR%%/php/annotate.js
-%%DATADIR%%/php/annotate_marker.php
-%%DATADIR%%/php/catalog.php
-%%DATADIR%%/php/catalog_genotypes.php
-%%DATADIR%%/php/constants.php.dist
-%%DATADIR%%/php/correct_genotype.php
-%%DATADIR%%/php/correct_genotypes.php
-%%DATADIR%%/php/db_functions.php
-%%DATADIR%%/php/export.js
-%%DATADIR%%/php/export_batch.php
-%%DATADIR%%/php/fst_view.php
-%%DATADIR%%/php/hapstat_view.php
-%%DATADIR%%/php/header.php
-%%DATADIR%%/php/images/caret-d.png
-%%DATADIR%%/php/images/caret-u.png
-%%DATADIR%%/php/images/excel_icon.png
-%%DATADIR%%/php/images/l-arrow-disabled.png
-%%DATADIR%%/php/images/l-arrow.png
-%%DATADIR%%/php/images/r-arrow-disabled.png
-%%DATADIR%%/php/images/r-arrow.png
-%%DATADIR%%/php/images/stacks_bg.png
-%%DATADIR%%/php/images/stacks_logo_rev_small.png
-%%DATADIR%%/php/index.php
-%%DATADIR%%/php/last_modified.php
-%%DATADIR%%/php/phist_view.php
-%%DATADIR%%/php/pop_view.php
-%%DATADIR%%/php/population_view.js
-%%DATADIR%%/php/samples.php
-%%DATADIR%%/php/sequence_blast.php
-%%DATADIR%%/php/stack_view.php
-%%DATADIR%%/php/stacks.css
-%%DATADIR%%/php/stacks.js
-%%DATADIR%%/php/stacks_functions.php
-%%DATADIR%%/php/sumstat_view.php
-%%DATADIR%%/php/tag.php
-%%DATADIR%%/php/tags.php
-%%DATADIR%%/php/version.php
-%%DATADIR%%/php/view_sequence.php
-%%DATADIR%%/sql/catalog_index.sql
-%%DATADIR%%/sql/chr_index.sql
-%%DATADIR%%/sql/mysql.cnf.dist
-%%DATADIR%%/sql/stacks.sql
-%%DATADIR%%/sql/tag_index.sql
-@dir %%DATADIR%%/php/export