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biology/mummer: update 4.0.0 → 4.0.1

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Reported by:	portscout
This commit is contained in:
Yuri Victorovich 2025-02-07 21:47:17 -08:00
parent 0e94c35c18
commit 297ffe8d7f
3 changed files with 50 additions and 43 deletions
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11
biology/mummer/Makefile
View file

@ -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>

6
biology/mummer/distinfo
View file

@ -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

76
biology/mummer/pkg-plist
View file

@ -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