From owner-svn-ports-all@FreeBSD.ORG Sat Apr 26 02:35:38 2014 Return-Path: Delivered-To: svn-ports-all@freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTPS id 9D79E108; Sat, 26 Apr 2014 02:35:38 +0000 (UTC) Received: from svn.freebsd.org (svn.freebsd.org [IPv6:2001:1900:2254:2068::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 8A4FD163F; Sat, 26 Apr 2014 02:35:38 +0000 (UTC) Received: from svn.freebsd.org ([127.0.1.70]) by svn.freebsd.org (8.14.8/8.14.8) with ESMTP id s3Q2ZcI8083330; Sat, 26 Apr 2014 02:35:38 GMT (envelope-from miwi@svn.freebsd.org) Received: (from miwi@localhost) by svn.freebsd.org (8.14.8/8.14.8/Submit) id s3Q2Zbil083326; Sat, 26 Apr 2014 02:35:37 GMT (envelope-from miwi@svn.freebsd.org) Message-Id: <201404260235.s3Q2Zbil083326@svn.freebsd.org> From: Martin Wilke Date: Sat, 26 Apr 2014 02:35:37 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r352216 - in head/biology/iolib: . files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.17 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 26 Apr 2014 02:35:38 -0000 Author: miwi Date: Sat Apr 26 02:35:37 2014 New Revision: 352216 URL: http://svnweb.freebsd.org/changeset/ports/352216 QAT: https://qat.redports.org/buildarchive/r352216/ Log: - Update to version 1.13.5 PR: 188863 Submitted by: ports fury Added: head/biology/iolib/files/patch-progs__scram_flgstat.c (contents, props changed) Modified: head/biology/iolib/Makefile head/biology/iolib/distinfo head/biology/iolib/pkg-plist Modified: head/biology/iolib/Makefile ============================================================================== --- head/biology/iolib/Makefile Sat Apr 26 02:33:55 2014 (r352215) +++ head/biology/iolib/Makefile Sat Apr 26 02:35:37 2014 (r352216) @@ -2,11 +2,9 @@ # $FreeBSD$ PORTNAME= io_lib -PORTVERSION= 1.13.0 -PORTREVISION= 1 +PORTVERSION= 1.13.5 CATEGORIES= biology -MASTER_SITES= SF -MASTER_SITE_SUBDIR= staden/${PORTNAME}/${PORTVERSION} +MASTER_SITES= SF/staden/${PORTNAME}/${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= General purpose trace file (and Experiment File) reading interface Modified: head/biology/iolib/distinfo ============================================================================== --- head/biology/iolib/distinfo Sat Apr 26 02:33:55 2014 (r352215) +++ head/biology/iolib/distinfo Sat Apr 26 02:35:37 2014 (r352216) @@ -1,2 +1,2 @@ -SHA256 (io_lib-1.13.0.tar.gz) = c3e0106802bd1a4a41427304944bcf11b7a4dd249cf470454a35d30cde13db5c -SIZE (io_lib-1.13.0.tar.gz) = 1522227 +SHA256 (io_lib-1.13.5.tar.gz) = 3e30f1e972d3d75c4efa54032ceca975cea9733ce1eef3982ee8a2b9f799ba56 +SIZE (io_lib-1.13.5.tar.gz) = 1808537 Added: head/biology/iolib/files/patch-progs__scram_flgstat.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/iolib/files/patch-progs__scram_flgstat.c Sat Apr 26 02:35:37 2014 (r352216) @@ -0,0 +1,10 @@ +--- progs/scram_flagstat.c.orig ++++ progs/scram_flagstat.c +@@ -44,6 +44,7 @@ + #include + #include + #include ++#include + + #if defined(__MINGW32__) + # include Modified: head/biology/iolib/pkg-plist ============================================================================== --- head/biology/iolib/pkg-plist Sat Apr 26 02:33:55 2014 (r352215) +++ head/biology/iolib/pkg-plist Sat Apr 26 02:35:37 2014 (r352216) @@ -1,8 +1,43 @@ +bin/append_sff +bin/convert_trace +bin/cram_dump +bin/cram_index +bin/extract_fastq +bin/extract_qual +bin/extract_seq +bin/get_comment +bin/hash_exp +bin/hash_extract +bin/hash_list +bin/hash_sff +bin/hash_tar +bin/index_tar +bin/io_lib-config +bin/makeSCF +bin/scf_dump +bin/scf_info +bin/scf_update +bin/scram_flagstat +bin/scram_merge +bin/scram_pileup +bin/scramble +bin/srf2fasta +bin/srf2fastq +bin/srf_dump_all +bin/srf_extract_hash +bin/srf_extract_linear +bin/srf_filter +bin/srf_index_hash +bin/srf_info +bin/srf_list +bin/trace_dump +bin/ztr_dump include/io_lib/Read.h include/io_lib/abi.h include/io_lib/alf.h include/io_lib/array.h include/io_lib/bam.h +include/io_lib/binning.h include/io_lib/compress.h include/io_lib/compression.h include/io_lib/cram.h @@ -11,6 +46,7 @@ include/io_lib/cram_decode.h include/io_lib/cram_encode.h include/io_lib/cram_index.h include/io_lib/cram_io.h +include/io_lib/cram_stats.h include/io_lib/cram_structs.h include/io_lib/deflate_interlaced.h include/io_lib/dstring.h @@ -33,57 +69,22 @@ include/io_lib/scf.h include/io_lib/scf_extras.h include/io_lib/scram.h include/io_lib/seqIOABI.h -include/io_lib/seqIOCTF.h include/io_lib/sff.h include/io_lib/srf.h include/io_lib/stdio_hack.h include/io_lib/string_alloc.h include/io_lib/tar_format.h +include/io_lib/thread_pool.h include/io_lib/traceType.h include/io_lib/translate.h include/io_lib/vlen.h include/io_lib/xalloc.h include/io_lib/zfio.h include/io_lib/ztr.h -bin/append_sff -bin/convert_trace -bin/cram_dump -bin/cram_index -bin/cram_to_sam -bin/extract_fastq -bin/extract_qual -bin/extract_seq -bin/get_comment -bin/hash_exp -bin/hash_extract -bin/hash_list -bin/hash_sff -bin/hash_tar -bin/index_tar -bin/io_lib-config -bin/makeSCF -bin/sam_convert -bin/sam_to_cram -bin/scf_dump -bin/scf_info -bin/scf_update -bin/scram_merge -bin/scramble -bin/srf2fasta -bin/srf2fastq -bin/srf_dump_all -bin/srf_extract_hash -bin/srf_extract_linear -bin/srf_filter -bin/srf_index_hash -bin/srf_info -bin/srf_list -bin/trace_dump -bin/ztr_dump lib/libstaden-read.a lib/libstaden-read.la lib/libstaden-read.so -lib/libstaden-read.so.3 +lib/libstaden-read.so.5 man/man1/scramble.1.gz man/man1/srf2fasta.1.gz man/man1/srf2fastq.1.gz