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ESMTPS id 4Yqk2n32QSz11LP; Sat, 08 Feb 2025 08:07:13 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 51887D19064095; Sat, 8 Feb 2025 08:07:13 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 51887DR9064092; Sat, 8 Feb 2025 08:07:13 GMT (envelope-from git) Date: Sat, 8 Feb 2025 08:07:13 GMT Message-Id: <202502080807.51887DR9064092@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Yuri Victorovich Subject: git: 297ffe8d7f3c - main - =?utf-8?Q?biology/mummer: update 4.0.0 =E2=86=92 4.0.1?= List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-dev-commits-ports-all@FreeBSD.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: yuri X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 297ffe8d7f3ca91b54e18673202abd03e6bc42bd Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=297ffe8d7f3ca91b54e18673202abd03e6bc42bd commit 297ffe8d7f3ca91b54e18673202abd03e6bc42bd Author: Yuri Victorovich AuthorDate: 2025-02-08 05:47:17 +0000 Commit: Yuri Victorovich 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 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