From d47daef533558ab4836532539b75cfc306fdd599 Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 4 Sep 2022 04:51:14 +0100 Subject: [PATCH] academic/genometools: Updated for version 1.6.2. Signed-off-by: Dave Woodfall --- academic/genometools/gcc10.patch | 88 --------------------- academic/genometools/genometools.SlackBuild | 7 +- academic/genometools/genometools.info | 6 +- 3 files changed, 5 insertions(+), 96 deletions(-) delete mode 100644 academic/genometools/gcc10.patch diff --git a/academic/genometools/gcc10.patch b/academic/genometools/gcc10.patch deleted file mode 100644 index 2c4edf1b74..0000000000 --- a/academic/genometools/gcc10.patch +++ /dev/null @@ -1,88 +0,0 @@ -From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001 -From: Sascha Steinbiss -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 -+ Copyright (c) 2008-2020 Sascha Steinbiss - 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 -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 diff --git a/academic/genometools/genometools.SlackBuild b/academic/genometools/genometools.SlackBuild index 9e55523524..47f6ca9adf 100644 --- a/academic/genometools/genometools.SlackBuild +++ b/academic/genometools/genometools.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for genometools -# Copyright 2014-2021 Petar Petrov slackalaxy@gmail.com +# Copyright 2014-2022 Petar Petrov slackalaxy@gmail.com # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -25,7 +25,7 @@ cd $(dirname $0) ; CWD=$(pwd) PRGNAM=genometools -VERSION=${VERSION:-1.6.1} +VERSION=${VERSION:-1.6.2} BUILD=${BUILD:-1} TAG=${TAG:-_SBo} PKGTYPE=${PKGTYPE:-tgz} @@ -90,9 +90,6 @@ find -L . \ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; -# Thanks Debian for the patch -patch -p1 -i $CWD/gcc10.patch - # Fix library and man pages path sed -i "s:lib/libgenometools:lib${LIBDIRSUFFIX}/libgenometools:g" Makefile sed -i "s:\$(prefix)/lib:\$(prefix)/lib${LIBDIRSUFFIX}:g" Makefile diff --git a/academic/genometools/genometools.info b/academic/genometools/genometools.info index 7692e762e8..cac6f3b826 100644 --- a/academic/genometools/genometools.info +++ b/academic/genometools/genometools.info @@ -1,8 +1,8 @@ PRGNAM="genometools" -VERSION="1.6.1" +VERSION="1.6.2" HOMEPAGE="http://genometools.org/" -DOWNLOAD="http://genometools.org/pub/genometools-1.6.1.tar.gz" -MD5SUM="1dc80df17be32973266f5a3601fc64b8" +DOWNLOAD="http://genometools.org/pub/genometools-1.6.2.tar.gz" +MD5SUM="431e34d5490148dbcbc95e3de7ac4b78" DOWNLOAD_x86_64="" MD5SUM_x86_64="" REQUIRES=""