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academic/genometools: add patch for gcc10 and fix build
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
This commit is contained in:
Petar Petrov
Willy Sudiarto Raharjo
parent
8493b05234
commit
4a818f17e3
2 changed files with 101 additions and 2 deletions
88
academic/genometools/gcc10.patch
Normal file
88
academic/genometools/gcc10.patch
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@ -0,0 +1,88 @@
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From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001
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From: Sascha Steinbiss <satta@debian.org>
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Date: Wed, 22 Apr 2020 21:59:57 +0200
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Subject: [PATCH 1/2] make sure to not ignore snprintf output
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GCC 10 will warn about the (here intended) silent string truncation
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done by snprintf() unless the return value is handled.
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Obviously this will break the build as we use -Werror. We
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circumvent the problem by checking the output value and printing a
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warning if we notice a truncation.
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---
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src/ltr/ltrdigest_file_out_stream.c | 17 ++++++++++++-----
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1 file changed, 12 insertions(+), 5 deletions(-)
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diff --git a/src/ltr/ltrdigest_file_out_stream.c b/src/ltr/ltrdigest_file_out_stream.c
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index 723b8cf9a..61325b693 100644
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--- a/src/ltr/ltrdigest_file_out_stream.c
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+++ b/src/ltr/ltrdigest_file_out_stream.c
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@@ -1,5 +1,5 @@
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/*
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- Copyright (c) 2008-2015 Sascha Steinbiss <sascha@steinbiss.name>
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+ Copyright (c) 2008-2020 Sascha Steinbiss <sascha@steinbiss.name>
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Copyright (c) 2008-2013 Center for Bioinformatics, University of Hamburg
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Permission to use, copy, modify, and distribute this software for any
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@@ -33,6 +33,7 @@
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#include "core/symbol.h"
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#include "core/undef_api.h"
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#include "core/unused_api.h"
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+#include "core/warning_api.h"
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#include "extended/extract_feature_sequence.h"
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#include "extended/feature_node.h"
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#include "extended/feature_node_iterator_api.h"
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@@ -416,6 +417,8 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
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if (!had_err) {
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GtRange rng;
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+ int ret = 0;
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+
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ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char));
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(void) snprintf(ls->element.seqid,
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GT_MIN((size_t) gt_str_length(sdesc),
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@@ -425,12 +428,16 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err)
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if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen)
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ls->element.seqid[ls->seqnamelen] = '\0';
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- (void) gt_ltrelement_format_description(&ls->element,
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- ls->seqnamelen,
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- desc,
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- (size_t) (GT_MAXFASTAHEADER-1));
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+ ret = gt_ltrelement_format_description(&ls->element,
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+ ls->seqnamelen,
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+ desc,
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+ (size_t) (GT_MAXFASTAHEADER-1));
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+ if (ret < 0) {
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+ gt_warning("FASTA header truncated: %s", desc);
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+ }
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gt_str_delete(sdesc);
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+
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/* output basic retrotransposon data */
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lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR);
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rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR);
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From 30ae36037228dc4ed174e8462f3489638e6f5e76 Mon Sep 17 00:00:00 2001
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From: Sascha Steinbiss <satta@debian.org>
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Date: Wed, 22 Apr 2020 22:01:00 +0200
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Subject: [PATCH 2/2] declare hashmap type as extern
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This fixes a build issue with GCC 10.
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Closes #941.
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---
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src/mgth/metagenomethreader.h | 2 +-
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1 file changed, 1 insertion(+), 1 deletion(-)
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diff --git a/src/mgth/metagenomethreader.h b/src/mgth/metagenomethreader.h
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index 92f16d498..7f76fffb9 100644
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--- a/src/mgth/metagenomethreader.h
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+++ b/src/mgth/metagenomethreader.h
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@@ -221,7 +221,7 @@ typedef struct
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} ParseStruct;
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/* specific access mode of queryhash */
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-DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp,,)
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+DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp, extern,)
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DECLARE_SAFE_DEREF(GtUword *, ulp)
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/* Funktion, mit der der Metagenomethreader gestartet wird
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@ -2,7 +2,7 @@
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# Slackware build script for genometools
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# Copyright 2014-2020 Petar Petrov slackalaxy@gmail.com
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# Copyright 2014-2021 Petar Petrov slackalaxy@gmail.com
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# All rights reserved.
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#
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# Redistribution and use of this script, with or without modification, is
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@ -66,11 +66,22 @@ rm -rf $PRGNAM-$VERSION
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tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
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cd $PRGNAM-$VERSION
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chown -R root:root .
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# This is a looping symlink that the 'find' step below complains about.
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# The only thing that is used from this location is 'sam.h', so let's
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# just make a proper folder and copy it there.
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rm src/external/samtools-0.1.18/samtools
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mkdir -p src/external/samtools-0.1.18/samtools
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cp src/external/samtools-0.1.18/sam.h src/external/samtools-0.1.18/samtools
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find -L . \
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\( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
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-o -perm 511 \) -exec chmod 755 {} \; -o \
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\( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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-o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
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# Thanks Debian for the patch
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patch -p1 -i $CWD/gcc10.patch
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# Fix library and man pages path
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sed -i "s:lib/libgenometools:lib${LIBDIRSUFFIX}/libgenometools:g" Makefile
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