From cd80a41fb1bb23a5b44ad044dd2f4acaec60c71c Mon Sep 17 00:00:00 2001
From: Mark Linimon <linimon@FreeBSD.org>
Date: Mon, 5 Nov 2018 19:47:42 +0000
Subject: [PATCH] Fix build failure with base GCC because of double typedefs.

PR:		232457
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
---
 .../files/patch-algo_blast_core_jumper.h      | 48 +++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h

diff --git a/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h b/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h
new file mode 100644
index 000000000000..52992b964820
--- /dev/null
+++ b/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h
@@ -0,0 +1,48 @@
+--- algo/blast/core/jumper.h.orig	2018-10-19 17:37:04 UTC
++++ algo/blast/core/jumper.h
+@@ -66,13 +66,13 @@ typedef struct JumperPrelimEditBlock
+ 
+ 
+ /** Gapped alignment data needed for jumper */
+-typedef struct JumperGapAlign
++struct JumperGapAlign
+ {
+     JumperPrelimEditBlock* left_prelim_block;
+     JumperPrelimEditBlock* right_prelim_block;
+     Uint4* table; /**< Table used for matching 4 bases in compressed subject
+                        to 4 bases in uncompressed query */
+-} JumperGapAlign;
++};
+ 
+ 
+ JumperGapAlign* JumperGapAlignFree(JumperGapAlign* jumper_align);
+@@ -90,11 +90,11 @@ typedef struct JumperEdit
+ 
+ 
+ /** Alignment edit script for gapped alignment */
+-typedef struct JumperEditsBlock
++struct JumperEditsBlock
+ {
+     JumperEdit* edits;
+     Int4 num_edits;
+-} JumperEditsBlock;
++};
+ 
+ 
+ JumperEditsBlock* JumperEditsBlockFree(JumperEditsBlock* block);
+@@ -262,13 +262,13 @@ JumperEditsBlock* JumperEditsBlockCombine(JumperEditsB
+                                           JumperEditsBlock** append);
+ 
+ /** Structure to save short unaligned subsequences outside an HSP */
+-typedef struct SequenceOverhangs
++struct SequenceOverhangs
+ {
+     Int4 left_len;    /**< Length of the left subsequence */
+     Int4 right_len;   /**< Length of the right subsequence */
+     Uint1* left;      /**< Left subsequence */
+     Uint1* right;     /**< Rught subsequence */
+-} SequenceOverhangs;
++};
+ 
+ SequenceOverhangs* SequenceOverhangsFree(SequenceOverhangs* overhangs);
+