git: 65febeef4968 - main - biology/mummer: update 4.0.0rc1.20240427 → 4.0.0

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Mon, 27 Jan 2025 09:58:09 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=65febeef4968d60797f986585512e42ba2daccd9

commit 65febeef4968d60797f986585512e42ba2daccd9
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-01-27 04:10:03 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-01-27 09:58:06 +0000

    biology/mummer: update 4.0.0rc1.20240427 → 4.0.0
---
 biology/mummer/Makefile  | 16 ++++++----
 biology/mummer/distinfo  |  6 ++--
 biology/mummer/pkg-plist | 76 ++++++++++++++++++++++++------------------------
 3 files changed, 51 insertions(+), 47 deletions(-)

diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index d4d16d14006c..609053e5bb22 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	mummer
 DISTVERSIONPREFIX=	v
-DISTVERSION=	4.0.0rc1.20240427
+DISTVERSION=	4.0.0
 CATEGORIES=	biology
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -13,23 +13,27 @@ LICENSE_FILE=	${WRKSRC}/LICENSE.md
 
 BUILD_DEPENDS=	yaggo:devel/yaggo
 
-USES=		autoreconf compiler:c++11-lang gmake libtool perl5 shebangfix
-GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--disable-static
+USES=		autoreconf compiler:c++17-lang gmake libtool perl5 shebangfix
 USE_LDCONFIG=	yes
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	${PORTNAME}4
-GH_TAGNAME=	7198b08 # devel branch since release is 4 years old
 
-INSTALL_TARGET=install-strip
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--disable-static
+
+INSTALL_TARGET=	install-strip
 
 SHEBANG_FILES=	scripts/*.pl
 perl_OLD_CMD=	__PERL_PATH
 _SHEBANG_REINPLACE_ARGS+=	-e "s|__BIN_DIR|${PREFIX}/bin|g;s|__AUX_BIN_DIR|${PREFIX}/libexec/mummer|g;s|__SCRIPT_DIR|${PREFIX}/libexec/mummer|g"
 
+TEST_TARGET=	check
+
 post-install:
 	# fix conflict with libgd
 	@${MV} ${STAGEDIR}${PREFIX}/bin/annotate ${STAGEDIR}${PREFIX}/bin/${PORTNAME}-annotate
 
+# 4.0.0: tests fail to compile, see https://github.com/mummer4/mummer/issues/221
+
 .include <bsd.port.mk>
diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo
index 72274d65cde3..0461d7dd860a 100644
--- a/biology/mummer/distinfo
+++ b/biology/mummer/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1730400797
-SHA256 (mummer4-mummer-v4.0.0rc1.20240427-7198b08_GH0.tar.gz) = f0daa3005fe528c5a6b9ef5f47846bbb232e893eead0518ba6a130dfab7aaaa1
-SIZE (mummer4-mummer-v4.0.0rc1.20240427-7198b08_GH0.tar.gz) = 18373638
+TIMESTAMP = 1737950649
+SHA256 (mummer4-mummer-v4.0.0_GH0.tar.gz) = 95b149764a078935d998f521ec7e623b200ea958cd34676fb609f440453d59a0
+SIZE (mummer4-mummer-v4.0.0_GH0.tar.gz) = 18392042
diff --git a/biology/mummer/pkg-plist b/biology/mummer/pkg-plist
index 15c04529bda8..14a83c5a171a 100644
--- a/biology/mummer/pkg-plist
+++ b/biology/mummer/pkg-plist
@@ -13,44 +13,44 @@ bin/show-coords
 bin/show-diff
 bin/show-snps
 bin/show-tiling
-include/mummer-4.0.0rc1/include/compactsufsort/compactsufsort.hpp
-include/mummer-4.0.0rc1/include/compactsufsort/compactsufsort_imp.hpp
-include/mummer-4.0.0rc1/include/compactsufsort/const_iterator_traits.hpp
-include/mummer-4.0.0rc1/include/compactsufsort/divsufsort_private.h
-include/mummer-4.0.0rc1/include/compactsufsort/said_traits.hpp
-include/mummer-4.0.0rc1/include/compactsufsort/sssort_imp.hpp
-include/mummer-4.0.0rc1/include/compactsufsort/trsort_imp.hpp
-include/mummer-4.0.0rc1/include/jellyfish/circular_buffer.hpp
-include/mummer-4.0.0rc1/include/jellyfish/cooperative_pool2.hpp
-include/mummer-4.0.0rc1/include/jellyfish/cpp_array.hpp
-include/mummer-4.0.0rc1/include/jellyfish/divisor.hpp
-include/mummer-4.0.0rc1/include/jellyfish/stream_manager.hpp
-include/mummer-4.0.0rc1/include/jellyfish/whole_sequence_parser.hpp
-include/mummer-4.0.0rc1/include/mt_skip_list/common.hpp
-include/mummer-4.0.0rc1/include/mt_skip_list/set.hpp
-include/mummer-4.0.0rc1/include/mummer/48bit_index.hpp
-include/mummer-4.0.0rc1/include/mummer/48bit_iterator.hpp
-include/mummer-4.0.0rc1/include/mummer/const_iterator_traits.hpp
-include/mummer-4.0.0rc1/include/mummer/delta.hh
-include/mummer-4.0.0rc1/include/mummer/dset.hpp
-include/mummer-4.0.0rc1/include/mummer/fasta.hpp
-include/mummer-4.0.0rc1/include/mummer/mgaps.hh
-include/mummer-4.0.0rc1/include/mummer/nucmer.hpp
-include/mummer-4.0.0rc1/include/mummer/openmp_qsort.hpp
-include/mummer-4.0.0rc1/include/mummer/postnuc.hh
-include/mummer-4.0.0rc1/include/mummer/redirect_to_pager.hpp
-include/mummer-4.0.0rc1/include/mummer/sparseSA.hpp
-include/mummer-4.0.0rc1/include/mummer/sparseSA_imp.hpp
-include/mummer-4.0.0rc1/include/mummer/sw_align.hh
-include/mummer-4.0.0rc1/include/mummer/sw_alignscore.hh
-include/mummer-4.0.0rc1/include/mummer/tigrinc.hh
-include/mummer-4.0.0rc1/include/mummer/timer.hpp
-include/mummer-4.0.0rc1/include/mummer/translate.hh
-include/mummer-4.0.0rc1/include/thread_pipe.hpp
-include/mummer-4.0.0rc1/include/thread_pipe/circular_buffer.hpp
-include/mummer-4.0.0rc1/include/thread_pipe/cooperative_pool2.hpp
-include/mummer-4.0.0rc1/include/thread_pipe/divisor.hpp
-include/mummer-4.0.0rc1/include/thread_pipe/traits.hpp
+include/mummer-4.0.0/include/compactsufsort/compactsufsort.hpp
+include/mummer-4.0.0/include/compactsufsort/compactsufsort_imp.hpp
+include/mummer-4.0.0/include/compactsufsort/const_iterator_traits.hpp
+include/mummer-4.0.0/include/compactsufsort/divsufsort_private.h
+include/mummer-4.0.0/include/compactsufsort/said_traits.hpp
+include/mummer-4.0.0/include/compactsufsort/sssort_imp.hpp
+include/mummer-4.0.0/include/compactsufsort/trsort_imp.hpp
+include/mummer-4.0.0/include/jellyfish/circular_buffer.hpp
+include/mummer-4.0.0/include/jellyfish/cooperative_pool2.hpp
+include/mummer-4.0.0/include/jellyfish/cpp_array.hpp
+include/mummer-4.0.0/include/jellyfish/divisor.hpp
+include/mummer-4.0.0/include/jellyfish/stream_manager.hpp
+include/mummer-4.0.0/include/jellyfish/whole_sequence_parser.hpp
+include/mummer-4.0.0/include/mt_skip_list/common.hpp
+include/mummer-4.0.0/include/mt_skip_list/set.hpp
+include/mummer-4.0.0/include/mummer/48bit_index.hpp
+include/mummer-4.0.0/include/mummer/48bit_iterator.hpp
+include/mummer-4.0.0/include/mummer/const_iterator_traits.hpp
+include/mummer-4.0.0/include/mummer/delta.hh
+include/mummer-4.0.0/include/mummer/dset.hpp
+include/mummer-4.0.0/include/mummer/fasta.hpp
+include/mummer-4.0.0/include/mummer/mgaps.hh
+include/mummer-4.0.0/include/mummer/nucmer.hpp
+include/mummer-4.0.0/include/mummer/openmp_qsort.hpp
+include/mummer-4.0.0/include/mummer/postnuc.hh
+include/mummer-4.0.0/include/mummer/redirect_to_pager.hpp
+include/mummer-4.0.0/include/mummer/sparseSA.hpp
+include/mummer-4.0.0/include/mummer/sparseSA_imp.hpp
+include/mummer-4.0.0/include/mummer/sw_align.hh
+include/mummer-4.0.0/include/mummer/sw_alignscore.hh
+include/mummer-4.0.0/include/mummer/tigrinc.hh
+include/mummer-4.0.0/include/mummer/timer.hpp
+include/mummer-4.0.0/include/mummer/translate.hh
+include/mummer-4.0.0/include/thread_pipe.hpp
+include/mummer-4.0.0/include/thread_pipe/circular_buffer.hpp
+include/mummer-4.0.0/include/thread_pipe/cooperative_pool2.hpp
+include/mummer-4.0.0/include/thread_pipe/divisor.hpp
+include/mummer-4.0.0/include/thread_pipe/traits.hpp
 lib/libumdmummer.so
 lib/libumdmummer.so.0
 lib/libumdmummer.so.0.0.0