Index: head/biology/jellyfish/Makefile =================================================================== --- head/biology/jellyfish/Makefile (revision 428953) +++ head/biology/jellyfish/Makefile (revision 428954) @@ -1,39 +1,40 @@ # Created by: Jason Bacon # $FreeBSD$ PORTNAME= jellyfish -PORTVERSION= 2.2.4 +PORTVERSION= 2.2.6 DISTVERSIONPREFIX= v CATEGORIES= biology MAINTAINER= bacon4000@gmail.com COMMENT= Fast, memory-efficient counting of k-mers in DNA LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= yaggo:devel/yaggo GNU_CONFIGURE= yes -USES= autoreconf compiler:c++11-lib gmake \ - libtool pathfix pkgconfig +USES= autoreconf compiler:c++11-lib gmake libtool pathfix pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= gmarcais GH_PROJECT= Jellyfish INSTALL_TARGET= install-strip -BROKEN_FreeBSD_9_i386= multiple code issues on i386 < 10.0-RELEASE +PLIST_SUB= VER=${PORTVERSION} + +BROKEN_FreeBSD_9_i386= Multiple code issues on i386 < 10.0-RELEASE BROKEN_aarch64= Fails to compile: error: variable res is uninitialized .include # SSE code assumes amd64 features .if ${ARCH} != "amd64" CONFIGURE_ARGS+=--without-sse .endif .include Index: head/biology/jellyfish/distinfo =================================================================== --- head/biology/jellyfish/distinfo (revision 428953) +++ head/biology/jellyfish/distinfo (revision 428954) @@ -1,2 +1,3 @@ -SHA256 (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 44b6478aed63b859b8287d72b4f9bfb5d513fed334efbc8a9e5783da12ecb3ec -SIZE (gmarcais-Jellyfish-v2.2.4_GH0.tar.gz) = 658653 +TIMESTAMP = 1482069678 +SHA256 (gmarcais-Jellyfish-v2.2.6_GH0.tar.gz) = 800bc60aaec273dc04296ee7493e714457f2fe88551f76693e5d9f9a679dd35e +SIZE (gmarcais-Jellyfish-v2.2.6_GH0.tar.gz) = 660858 Index: head/biology/jellyfish/pkg-plist =================================================================== --- head/biology/jellyfish/pkg-plist (revision 428953) +++ head/biology/jellyfish/pkg-plist (revision 428954) @@ -1,55 +1,55 @@ bin/jellyfish -include/jellyfish-2.2.4/jellyfish/allocators_mmap.hpp -include/jellyfish-2.2.4/jellyfish/atomic_bits_array.hpp -include/jellyfish-2.2.4/jellyfish/atomic_field.hpp -include/jellyfish-2.2.4/jellyfish/atomic_gcc.hpp -include/jellyfish-2.2.4/jellyfish/backtrace.hpp -include/jellyfish-2.2.4/jellyfish/binary_dumper.hpp -include/jellyfish-2.2.4/jellyfish/bloom_common.hpp -include/jellyfish-2.2.4/jellyfish/bloom_counter2.hpp -include/jellyfish-2.2.4/jellyfish/bloom_filter.hpp -include/jellyfish-2.2.4/jellyfish/circular_buffer.hpp -include/jellyfish-2.2.4/jellyfish/compare_and_swap.hpp -include/jellyfish-2.2.4/jellyfish/cooperative_pool.hpp -include/jellyfish-2.2.4/jellyfish/cooperative_pool2.hpp -include/jellyfish-2.2.4/jellyfish/cpp_array.hpp -include/jellyfish-2.2.4/jellyfish/divisor.hpp -include/jellyfish-2.2.4/jellyfish/dumper.hpp -include/jellyfish-2.2.4/jellyfish/err.hpp -include/jellyfish-2.2.4/jellyfish/file_header.hpp -include/jellyfish-2.2.4/jellyfish/generator_manager.hpp -include/jellyfish-2.2.4/jellyfish/generic_file_header.hpp -include/jellyfish-2.2.4/jellyfish/hash_counter.hpp -include/jellyfish-2.2.4/jellyfish/int128.hpp -include/jellyfish-2.2.4/jellyfish/jellyfish.hpp -include/jellyfish-2.2.4/jellyfish/json.h -include/jellyfish-2.2.4/jellyfish/large_hash_array.hpp -include/jellyfish-2.2.4/jellyfish/large_hash_iterator.hpp -include/jellyfish-2.2.4/jellyfish/locks_pthread.hpp -include/jellyfish-2.2.4/jellyfish/mapped_file.hpp -include/jellyfish-2.2.4/jellyfish/mer_dna.hpp -include/jellyfish-2.2.4/jellyfish/mer_dna_bloom_counter.hpp -include/jellyfish-2.2.4/jellyfish/mer_heap.hpp -include/jellyfish-2.2.4/jellyfish/mer_iterator.hpp -include/jellyfish-2.2.4/jellyfish/mer_overlap_sequence_parser.hpp -include/jellyfish-2.2.4/jellyfish/mer_qual_iterator.hpp -include/jellyfish-2.2.4/jellyfish/misc.hpp -include/jellyfish-2.2.4/jellyfish/offsets_key_value.hpp -include/jellyfish-2.2.4/jellyfish/rectangular_binary_matrix.hpp -include/jellyfish-2.2.4/jellyfish/simple_circular_buffer.hpp -include/jellyfish-2.2.4/jellyfish/sorted_dumper.hpp -include/jellyfish-2.2.4/jellyfish/stdio_filebuf.hpp -include/jellyfish-2.2.4/jellyfish/storage.hpp -include/jellyfish-2.2.4/jellyfish/stream_iterator.hpp -include/jellyfish-2.2.4/jellyfish/stream_manager.hpp -include/jellyfish-2.2.4/jellyfish/text_dumper.hpp -include/jellyfish-2.2.4/jellyfish/thread_exec.hpp -include/jellyfish-2.2.4/jellyfish/time.hpp -include/jellyfish-2.2.4/jellyfish/token_ring.hpp -include/jellyfish-2.2.4/jellyfish/whole_sequence_parser.hpp +include/jellyfish-%%VER%%/jellyfish/allocators_mmap.hpp +include/jellyfish-%%VER%%/jellyfish/atomic_bits_array.hpp +include/jellyfish-%%VER%%/jellyfish/atomic_field.hpp +include/jellyfish-%%VER%%/jellyfish/atomic_gcc.hpp +include/jellyfish-%%VER%%/jellyfish/backtrace.hpp +include/jellyfish-%%VER%%/jellyfish/binary_dumper.hpp +include/jellyfish-%%VER%%/jellyfish/bloom_common.hpp +include/jellyfish-%%VER%%/jellyfish/bloom_counter2.hpp +include/jellyfish-%%VER%%/jellyfish/bloom_filter.hpp +include/jellyfish-%%VER%%/jellyfish/circular_buffer.hpp +include/jellyfish-%%VER%%/jellyfish/compare_and_swap.hpp +include/jellyfish-%%VER%%/jellyfish/cooperative_pool.hpp +include/jellyfish-%%VER%%/jellyfish/cooperative_pool2.hpp +include/jellyfish-%%VER%%/jellyfish/cpp_array.hpp +include/jellyfish-%%VER%%/jellyfish/divisor.hpp +include/jellyfish-%%VER%%/jellyfish/dumper.hpp +include/jellyfish-%%VER%%/jellyfish/err.hpp +include/jellyfish-%%VER%%/jellyfish/file_header.hpp +include/jellyfish-%%VER%%/jellyfish/generator_manager.hpp +include/jellyfish-%%VER%%/jellyfish/generic_file_header.hpp +include/jellyfish-%%VER%%/jellyfish/hash_counter.hpp +include/jellyfish-%%VER%%/jellyfish/int128.hpp +include/jellyfish-%%VER%%/jellyfish/jellyfish.hpp +include/jellyfish-%%VER%%/jellyfish/json.h +include/jellyfish-%%VER%%/jellyfish/large_hash_array.hpp +include/jellyfish-%%VER%%/jellyfish/large_hash_iterator.hpp +include/jellyfish-%%VER%%/jellyfish/locks_pthread.hpp +include/jellyfish-%%VER%%/jellyfish/mapped_file.hpp +include/jellyfish-%%VER%%/jellyfish/mer_dna.hpp +include/jellyfish-%%VER%%/jellyfish/mer_dna_bloom_counter.hpp +include/jellyfish-%%VER%%/jellyfish/mer_heap.hpp +include/jellyfish-%%VER%%/jellyfish/mer_iterator.hpp +include/jellyfish-%%VER%%/jellyfish/mer_overlap_sequence_parser.hpp +include/jellyfish-%%VER%%/jellyfish/mer_qual_iterator.hpp +include/jellyfish-%%VER%%/jellyfish/misc.hpp +include/jellyfish-%%VER%%/jellyfish/offsets_key_value.hpp +include/jellyfish-%%VER%%/jellyfish/rectangular_binary_matrix.hpp +include/jellyfish-%%VER%%/jellyfish/simple_circular_buffer.hpp +include/jellyfish-%%VER%%/jellyfish/sorted_dumper.hpp +include/jellyfish-%%VER%%/jellyfish/stdio_filebuf.hpp +include/jellyfish-%%VER%%/jellyfish/storage.hpp +include/jellyfish-%%VER%%/jellyfish/stream_iterator.hpp +include/jellyfish-%%VER%%/jellyfish/stream_manager.hpp +include/jellyfish-%%VER%%/jellyfish/text_dumper.hpp +include/jellyfish-%%VER%%/jellyfish/thread_exec.hpp +include/jellyfish-%%VER%%/jellyfish/time.hpp +include/jellyfish-%%VER%%/jellyfish/token_ring.hpp +include/jellyfish-%%VER%%/jellyfish/whole_sequence_parser.hpp lib/libjellyfish-2.0.a lib/libjellyfish-2.0.so lib/libjellyfish-2.0.so.2 lib/libjellyfish-2.0.so.2.0.0 libdata/pkgconfig/jellyfish-2.0.pc man/man1/jellyfish.1.gz