From owner-svn-ports-head@freebsd.org Mon Dec 19 16:52:36 2016 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 0D0E8C881E0; Mon, 19 Dec 2016 16:52:36 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id C1D9519D2; Mon, 19 Dec 2016 16:52:35 +0000 (UTC) (envelope-from jrm@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id uBJGqY9D069638; Mon, 19 Dec 2016 16:52:34 GMT (envelope-from jrm@FreeBSD.org) Received: (from jrm@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id uBJGqYdB069635; Mon, 19 Dec 2016 16:52:34 GMT (envelope-from jrm@FreeBSD.org) Message-Id: <201612191652.uBJGqYdB069635@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jrm set sender to jrm@FreeBSD.org using -f From: Joseph Mingrone Date: Mon, 19 Dec 2016 16:52:34 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r428954 - head/biology/jellyfish X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 19 Dec 2016 16:52:36 -0000 Author: jrm Date: Mon Dec 19 16:52:34 2016 New Revision: 428954 URL: https://svnweb.freebsd.org/changeset/ports/428954 Log: biology/jellyfish: Update to version 2.2.6 Upstream changes since version 2.2.4: - Fix compilation warnings/errors with newer version of gcc (5.3 & 6.1). - Fix bug in parsing function that made it stop on sequences that consist of only empty lines. - New methods in bindings to enumerate the mers of a string. Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8204 Modified: head/biology/jellyfish/Makefile head/biology/jellyfish/distinfo head/biology/jellyfish/pkg-plist Modified: head/biology/jellyfish/Makefile ============================================================================== --- head/biology/jellyfish/Makefile Mon Dec 19 16:39:41 2016 (r428953) +++ head/biology/jellyfish/Makefile Mon Dec 19 16:52:34 2016 (r428954) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= jellyfish -PORTVERSION= 2.2.4 +PORTVERSION= 2.2.6 DISTVERSIONPREFIX= v CATEGORIES= biology @@ -16,8 +16,7 @@ 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 @@ -26,7 +25,9 @@ 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 Modified: head/biology/jellyfish/distinfo ============================================================================== --- head/biology/jellyfish/distinfo Mon Dec 19 16:39:41 2016 (r428953) +++ head/biology/jellyfish/distinfo Mon Dec 19 16:52:34 2016 (r428954) @@ -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 Modified: head/biology/jellyfish/pkg-plist ============================================================================== --- head/biology/jellyfish/pkg-plist Mon Dec 19 16:39:41 2016 (r428953) +++ head/biology/jellyfish/pkg-plist Mon Dec 19 16:52:34 2016 (r428954) @@ -1,52 +1,52 @@ 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