Date: Mon, 5 Nov 2018 19:47:43 +0000 (UTC) From: Mark Linimon <linimon@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r484211 - head/biology/ncbi-toolkit/files Message-ID: <201811051947.wA5JlhJb086973@repo.freebsd.org>
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Author: linimon Date: Mon Nov 5 19:47:42 2018 New Revision: 484211 URL: https://svnweb.freebsd.org/changeset/ports/484211 Log: Fix build failure with base GCC because of double typedefs. PR: 232457 Submitted by: Piotr Kubaj Approved by: portmgr (tier-2 blanket) Added: head/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h (contents, props changed) Added: head/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ncbi-toolkit/files/patch-algo_blast_core_jumper.h Mon Nov 5 19:47:42 2018 (r484211) @@ -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); +
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