[med-svn] [Git][med-team/genometools][master] add patch to fix build on GCC10

[Sascha Steinbiss]

Sascha Steinbiss pushed to branch master at Debian Med / genometools


Commits:
bb3bf8ab by Sascha Steinbiss at 2020-07-22T13:33:29+02:00
add patch to fix build on GCC10

- - - - -


4 changed files:

- debian/changelog
- debian/patches/adding_soname
- + debian/patches/gcc10.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+genometools (1.6.1+ds-3) unstable; urgency=medium
+
+  * Add patch to fix build on GCC 10.
+    Closes: #957268
+
+ -- Sascha Steinbiss <satta at debian.org>  Wed, 22 Jul 2020 13:00:06 +0200
+
 genometools (1.6.1+ds-2) unstable; urgency=medium
 
   * Use static images for AnnotationSketch documentation.


=====================================
debian/patches/adding_soname
=====================================
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss <steinbiss at zbh.uni-hamburg.de>
  
  define PROGRAM_template
  $(1): $(2)
-@@ -1003,7 +1005,8 @@
+@@ -999,7 +1001,8 @@
  	$(RANLIB) $(prefix)/lib/libgenometools.a
  endif
  ifneq ($(sharedlib),no)


=====================================
debian/patches/gcc10.patch
=====================================
@@ -0,0 +1,88 @@
+From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001
+From: Sascha Steinbiss <satta at 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 at steinbiss.name>
++  Copyright (c) 2008-2020 Sascha Steinbiss <sascha at 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 at 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


=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ split-manuals
 use-mx32
 gtdoc-traverse-sorted
 ignore-m32-m64.patch
+gcc10.patch



View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/bb3bf8ab616752843b8cf4915e9998e3827198f4

-- 
View it on GitLab: https://salsa.debian.org/med-team/genometools/-/commit/bb3bf8ab616752843b8cf4915e9998e3827198f4
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