Date: Thu, 31 Oct 2024 19:28:16 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 8cae05937efc - main - biology/mummer: update 4.0.0beta2-2 =?utf-8?Q?=E2=86=92?= 4.0.0rc1.20240427 Message-ID: <202410311928.49VJSGX8052673@gitrepo.freebsd.org>
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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
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