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 <[email protected]> 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 <[email protected]> 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 <[email protected]> +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 <[email protected]> ++ Copyright (c) 2008-2020 Sascha Steinbiss <[email protected]> + 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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