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biology/mummer: update 4.0.0beta2-2 → 4.0.0rc1.20240427

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This commit is contained in:
Yuri Victorovich 2024-10-31 12:26:03 -07:00
parent 4c9739d1ae
commit 8cae05937e
4 changed files with 64 additions and 49 deletions
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19
biology/mummer/Makefile
View File

@ -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_GITHUB= yes
GH_ACCOUNT= ${PORTNAME}4
USE_LDCONFIG= yes
CONFLICTS_INSTALL= ??-libgd libgd
USE_GITHUB= yes
GH_ACCOUNT= ${PORTNAME}4
GH_TAGNAME= 7198b08 # devel branch since release is 4 years old
INSTALL_TARGET=install-strip
SHEBANG_FILES= scripts/*.pl
perl_OLD_CMD= __PERL_PATH
_SHEBANG_REINPLACE_ARGS+= -e "s|__BIN_DIR|${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>

6
biology/mummer/distinfo
View File

@ -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

8
biology/mummer/files/patch-development.mk Normal file
View File

@ -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

80
biology/mummer/pkg-plist
View File

@ -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