academic/genometools: Updated for version 1.6.2.

Signed-off-by: Dave Woodfall <dave@slackbuilds.org>

3 files changed, 5 insertions, 96 deletions

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 <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
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=""