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ESMTPS id 4YhP4K3MDmz7xp; Mon, 27 Jan 2025 09:58:09 +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 50R9w9B5057733; Mon, 27 Jan 2025 09:58:09 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 50R9w92t057729; Mon, 27 Jan 2025 09:58:09 GMT (envelope-from git) Date: Mon, 27 Jan 2025 09:58:09 GMT Message-Id: <202501270958.50R9w92t057729@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: 65febeef4968 - main - =?utf-8?Q?biology/mummer: update 4.0.0rc1.20240427 =E2=86=92 4.0.0?= List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@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: 65febeef4968d60797f986585512e42ba2daccd9 Auto-Submitted: auto-generated The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=65febeef4968d60797f986585512e42ba2daccd9 commit 65febeef4968d60797f986585512e42ba2daccd9 Author: Yuri Victorovich AuthorDate: 2025-01-27 04:10:03 +0000 Commit: Yuri Victorovich 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 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