git: 8cae05937efc - main - biology/mummer: update 4.0.0beta2-2 → 4.0.0rc1.20240427

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Thu, 31 Oct 2024 19:28:16 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8cae05937efc283df4b3ac2cb18fddc66e8a16a9

commit 8cae05937efc283df4b3ac2cb18fddc66e8a16a9
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2024-10-31 19:26:03 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2024-10-31 19:28:12 +0000

    biology/mummer: update 4.0.0beta2-2 → 4.0.0rc1.20240427
---
 biology/mummer/Makefile                   | 17 ++++---
 biology/mummer/distinfo                   |  6 +--
 biology/mummer/files/patch-development.mk |  8 ++++
 biology/mummer/pkg-plist                  | 80 ++++++++++++++++---------------
 4 files changed, 63 insertions(+), 48 deletions(-)

diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index 94f25d9b70c4..d4d16d14006c 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -1,13 +1,12 @@
 PORTNAME=	mummer
 DISTVERSIONPREFIX=	v
-DISTVERSION=	4.0.0beta2-2
-PORTREVISION=	3
-DISTVERSIONSUFFIX=	-g277dac5
+DISTVERSION=	4.0.0rc1.20240427
 CATEGORIES=	biology
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Modular system for rapid whole genome alignment
-WWW=		https://mummer.sourceforge.net/
+WWW=		https://mummer.sourceforge.net/ \
+		https://github.com/mummer4/mummer
 
 LICENSE=	ART10
 LICENSE_FILE=	${WRKSRC}/LICENSE.md
@@ -17,14 +16,20 @@ BUILD_DEPENDS=	yaggo:devel/yaggo
 USES=		autoreconf compiler:c++11-lang gmake libtool perl5 shebangfix
 GNU_CONFIGURE=	yes
 CONFIGURE_ARGS=	--disable-static
+USE_LDCONFIG=	yes
+
 USE_GITHUB=	yes
 GH_ACCOUNT=	${PORTNAME}4
-USE_LDCONFIG=	yes
+GH_TAGNAME=	7198b08 # devel branch since release is 4 years old
 
-CONFLICTS_INSTALL=	??-libgd libgd
+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"
 
+post-install:
+	# fix conflict with libgd
+	@${MV} ${STAGEDIR}${PREFIX}/bin/annotate ${STAGEDIR}${PREFIX}/bin/${PORTNAME}-annotate
+
 .include <bsd.port.mk>
diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo
index fbf62e1b29dd..72274d65cde3 100644
--- a/biology/mummer/distinfo
+++ b/biology/mummer/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1544513160
-SHA256 (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 4b77fb57f0e7994ed0cb9886de23ce620b89cb16734df82ba492dbc750e387f1
-SIZE (mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz) = 18369428
+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
diff --git a/biology/mummer/files/patch-development.mk b/biology/mummer/files/patch-development.mk
new file mode 100644
index 000000000000..0be7e3dece43
--- /dev/null
+++ b/biology/mummer/files/patch-development.mk
@@ -0,0 +1,8 @@
+--- development.mk.orig	2024-10-31 18:57:40 UTC
++++ development.mk
+@@ -1,4 +1,4 @@
+-AM_CXXFLAGS += -Werror
++#AM_CXXFLAGS += -Werror
+ 
+ # Count lines of code
+ .PHONY: cloc
diff --git a/biology/mummer/pkg-plist b/biology/mummer/pkg-plist
index 8e4946d83c05..15c04529bda8 100644
--- a/biology/mummer/pkg-plist
+++ b/biology/mummer/pkg-plist
@@ -1,9 +1,9 @@
-bin/annotate
 bin/combineMUMs
 bin/delta-filter
 bin/dnadiff
 bin/exact-tandems
 bin/mummer
+bin/mummer-annotate
 bin/mummerplot
 bin/nucmer
 bin/promer
@@ -13,44 +13,44 @@ bin/show-coords
 bin/show-diff
 bin/show-snps
 bin/show-tiling
-include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort.hpp
-include/mummer-4.0.0beta2/include/compactsufsort/compactsufsort_imp.hpp
-include/mummer-4.0.0beta2/include/compactsufsort/const_iterator_traits.hpp
-include/mummer-4.0.0beta2/include/compactsufsort/divsufsort_private.h
-include/mummer-4.0.0beta2/include/compactsufsort/said_traits.hpp
-include/mummer-4.0.0beta2/include/compactsufsort/sssort_imp.hpp
-include/mummer-4.0.0beta2/include/compactsufsort/trsort_imp.hpp
-include/mummer-4.0.0beta2/include/jellyfish/circular_buffer.hpp
-include/mummer-4.0.0beta2/include/jellyfish/cooperative_pool2.hpp
-include/mummer-4.0.0beta2/include/jellyfish/cpp_array.hpp
-include/mummer-4.0.0beta2/include/jellyfish/divisor.hpp
-include/mummer-4.0.0beta2/include/jellyfish/stream_manager.hpp
-include/mummer-4.0.0beta2/include/jellyfish/whole_sequence_parser.hpp
-include/mummer-4.0.0beta2/include/mt_skip_list/common.hpp
-include/mummer-4.0.0beta2/include/mt_skip_list/set.hpp
-include/mummer-4.0.0beta2/include/mummer/48bit_index.hpp
-include/mummer-4.0.0beta2/include/mummer/48bit_iterator.hpp
-include/mummer-4.0.0beta2/include/mummer/const_iterator_traits.hpp
-include/mummer-4.0.0beta2/include/mummer/delta.hh
-include/mummer-4.0.0beta2/include/mummer/dset.hpp
-include/mummer-4.0.0beta2/include/mummer/fasta.hpp
-include/mummer-4.0.0beta2/include/mummer/mgaps.hh
-include/mummer-4.0.0beta2/include/mummer/nucmer.hpp
-include/mummer-4.0.0beta2/include/mummer/openmp_qsort.hpp
-include/mummer-4.0.0beta2/include/mummer/postnuc.hh
-include/mummer-4.0.0beta2/include/mummer/redirect_to_pager.hpp
-include/mummer-4.0.0beta2/include/mummer/sparseSA.hpp
-include/mummer-4.0.0beta2/include/mummer/sparseSA_imp.hpp
-include/mummer-4.0.0beta2/include/mummer/sw_align.hh
-include/mummer-4.0.0beta2/include/mummer/sw_alignscore.hh
-include/mummer-4.0.0beta2/include/mummer/tigrinc.hh
-include/mummer-4.0.0beta2/include/mummer/timer.hpp
-include/mummer-4.0.0beta2/include/mummer/translate.hh
-include/mummer-4.0.0beta2/include/thread_pipe.hpp
-include/mummer-4.0.0beta2/include/thread_pipe/circular_buffer.hpp
-include/mummer-4.0.0beta2/include/thread_pipe/cooperative_pool2.hpp
-include/mummer-4.0.0beta2/include/thread_pipe/divisor.hpp
-include/mummer-4.0.0beta2/include/thread_pipe/traits.hpp
+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
 lib/libumdmummer.so
 lib/libumdmummer.so.0
 lib/libumdmummer.so.0.0.0
@@ -58,6 +58,8 @@ lib/mummer/Foundation.pm
 lib/mummer/tandem-repeat.awk
 libdata/pkgconfig/mummer.pc
 libexec/mummer/mgaps
+libexec/mummer/nucmer_ori
 libexec/mummer/postnuc
 libexec/mummer/postpro
+libexec/mummer/prenuc
 libexec/mummer/prepro