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From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001
From: Sascha Steinbiss <satta@debian.org>
Date: Wed, 22 Apr 2020 21:59:57 +0200
Subject: [PATCH 1/2] make sure to not ignore snprintf output
GCC 10 will warn about the (here intended) silent string truncation
done by snprintf() unless the return value is handled.
Obviously this will break the build as we use -Werror. We
circumvent the problem by checking the output value and printing a
warning if we notice a truncation.
---
src/ltr/ltrdigest_file_out_stream.c | 17 ++++++++++++-----
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/src/ltr/ltrdigest_file_out_stream.c b/src/ltr/ltrdigest_file_out_stream.c
index 723b8cf9a..61325b693 100644
--- a/src/ltr/ltrdigest_file_out_stream.c
+++ b/src/ltr/ltrdigest_file_out_stream.c
@@ -1,5 +1,5 @@
/*
- Copyright (c) 2008-2015 Sascha Steinbiss <sascha@steinbiss.name>
+ Copyright (c) 2008-2020 Sascha Steinbiss <sascha@steinbiss.name>
Copyright (c) 2008-2013 Center for Bioinformatics, University of Hamburg
Permission to use, copy, modify, and distribute this software for any
@@ -33,6 +33,7 @@
#include "core/symbol.h"
#include "core/undef_api.h"
#include "core/unused_api.h"
+#include "core/warning_api.h"
#include "extended/extract_feature_sequence.h"
#include "extended/feature_node.h"
#include "extended/feature_node_iterator_api.h"
@@ -416,6 +417,8 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
if (!had_err) {
GtRange rng;
+ int ret = 0;
+
ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char));
(void) snprintf(ls->element.seqid,
GT_MIN((size_t) gt_str_length(sdesc),
@@ -425,12 +428,16 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen)
ls->element.seqid[ls->seqnamelen] = '\0';
- (void) gt_ltrelement_format_description(&ls->element,
- ls->seqnamelen,
- desc,
- (size_t) (GT_MAXFASTAHEADER-1));
+ ret = gt_ltrelement_format_description(&ls->element,
+ ls->seqnamelen,
+ desc,
+ (size_t) (GT_MAXFASTAHEADER-1));
+ if (ret < 0) {
+ gt_warning("FASTA header truncated: %s", desc);
+ }
gt_str_delete(sdesc);
+
/* output basic retrotransposon data */
lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR);
rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR);
From 30ae36037228dc4ed174e8462f3489638e6f5e76 Mon Sep 17 00:00:00 2001
From: Sascha Steinbiss <satta@debian.org>
Date: Wed, 22 Apr 2020 22:01:00 +0200
Subject: [PATCH 2/2] declare hashmap type as extern
This fixes a build issue with GCC 10.
Closes #941.
---
src/mgth/metagenomethreader.h | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/mgth/metagenomethreader.h b/src/mgth/metagenomethreader.h
index 92f16d498..7f76fffb9 100644
--- a/src/mgth/metagenomethreader.h
+++ b/src/mgth/metagenomethreader.h
@@ -221,7 +221,7 @@ typedef struct
} ParseStruct;
/* specific access mode of queryhash */
-DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp,,)
+DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp, extern,)
DECLARE_SAFE_DEREF(GtUword *, ulp)
/* Funktion, mit der der Metagenomethreader gestartet wird
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