git: 297ffe8d7f3c - main - biology/mummer: update 4.0.0 → 4.0.1

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sat, 08 Feb 2025 08:07:13 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=297ffe8d7f3ca91b54e18673202abd03e6bc42bd

commit 297ffe8d7f3ca91b54e18673202abd03e6bc42bd
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2025-02-08 05:47:17 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2025-02-08 08:07:06 +0000

    biology/mummer: update 4.0.0 → 4.0.1
    
    Reported by:    portscout
---
 biology/mummer/Makefile  | 11 +++++--
 biology/mummer/distinfo  |  6 ++--
 biology/mummer/pkg-plist | 76 ++++++++++++++++++++++++------------------------
 3 files changed, 50 insertions(+), 43 deletions(-)

diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile
index 609053e5bb22..c60604a14f99 100644
--- a/biology/mummer/Makefile
+++ b/biology/mummer/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	mummer
 DISTVERSIONPREFIX=	v
-DISTVERSION=	4.0.0
+DISTVERSION=	4.0.1
 CATEGORIES=	biology
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -34,6 +34,13 @@ 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
+# tests as of 4.0.1, see https://github.com/mummer4/mummer/issues/224:
+# TOTAL: 9
+# PASS:  3
+# SKIP:  0
+# XFAIL: 0
+# FAIL:  6
+# XPASS: 0
+# ERROR: 0
 
 .include <bsd.port.mk>
diff --git a/biology/mummer/distinfo b/biology/mummer/distinfo
index 0461d7dd860a..e1e0842738fa 100644
--- a/biology/mummer/distinfo
+++ b/biology/mummer/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1737950649
-SHA256 (mummer4-mummer-v4.0.0_GH0.tar.gz) = 95b149764a078935d998f521ec7e623b200ea958cd34676fb609f440453d59a0
-SIZE (mummer4-mummer-v4.0.0_GH0.tar.gz) = 18392042
+TIMESTAMP = 1738977183
+SHA256 (mummer4-mummer-v4.0.1_GH0.tar.gz) = b866abcf75e0a24fbda8f8516defadfe523077d0d7303f941ff5d9673892eeab
+SIZE (mummer4-mummer-v4.0.1_GH0.tar.gz) = 18393280
diff --git a/biology/mummer/pkg-plist b/biology/mummer/pkg-plist
index 14a83c5a171a..0a5164b4a99a 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-4.0.0/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
+include/mummer-4.0.1/include/compactsufsort/compactsufsort.hpp
+include/mummer-4.0.1/include/compactsufsort/compactsufsort_imp.hpp
+include/mummer-4.0.1/include/compactsufsort/const_iterator_traits.hpp
+include/mummer-4.0.1/include/compactsufsort/divsufsort_private.h
+include/mummer-4.0.1/include/compactsufsort/said_traits.hpp
+include/mummer-4.0.1/include/compactsufsort/sssort_imp.hpp
+include/mummer-4.0.1/include/compactsufsort/trsort_imp.hpp
+include/mummer-4.0.1/include/jellyfish/circular_buffer.hpp
+include/mummer-4.0.1/include/jellyfish/cooperative_pool2.hpp
+include/mummer-4.0.1/include/jellyfish/cpp_array.hpp
+include/mummer-4.0.1/include/jellyfish/divisor.hpp
+include/mummer-4.0.1/include/jellyfish/stream_manager.hpp
+include/mummer-4.0.1/include/jellyfish/whole_sequence_parser.hpp
+include/mummer-4.0.1/include/mt_skip_list/common.hpp
+include/mummer-4.0.1/include/mt_skip_list/set.hpp
+include/mummer-4.0.1/include/mummer/48bit_index.hpp
+include/mummer-4.0.1/include/mummer/48bit_iterator.hpp
+include/mummer-4.0.1/include/mummer/const_iterator_traits.hpp
+include/mummer-4.0.1/include/mummer/delta.hh
+include/mummer-4.0.1/include/mummer/dset.hpp
+include/mummer-4.0.1/include/mummer/fasta.hpp
+include/mummer-4.0.1/include/mummer/mgaps.hh
+include/mummer-4.0.1/include/mummer/nucmer.hpp
+include/mummer-4.0.1/include/mummer/openmp_qsort.hpp
+include/mummer-4.0.1/include/mummer/postnuc.hh
+include/mummer-4.0.1/include/mummer/redirect_to_pager.hpp
+include/mummer-4.0.1/include/mummer/sparseSA.hpp
+include/mummer-4.0.1/include/mummer/sparseSA_imp.hpp
+include/mummer-4.0.1/include/mummer/sw_align.hh
+include/mummer-4.0.1/include/mummer/sw_alignscore.hh
+include/mummer-4.0.1/include/mummer/tigrinc.hh
+include/mummer-4.0.1/include/mummer/timer.hpp
+include/mummer-4.0.1/include/mummer/translate.hh
+include/mummer-4.0.1/include/thread_pipe.hpp
+include/mummer-4.0.1/include/thread_pipe/circular_buffer.hpp
+include/mummer-4.0.1/include/thread_pipe/cooperative_pool2.hpp
+include/mummer-4.0.1/include/thread_pipe/divisor.hpp
+include/mummer-4.0.1/include/thread_pipe/traits.hpp
 lib/libumdmummer.so
 lib/libumdmummer.so.0
 lib/libumdmummer.so.0.0.0