Date: Tue, 30 Apr 2013 15:41:49 +0000 (UTC) From: Frederic Culot <culot@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r316940 - in head/biology/iolib: . files Message-ID: <201304301541.r3UFfnGY089067@svn.freebsd.org>
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Author: culot Date: Tue Apr 30 15:41:49 2013 New Revision: 316940 URL: http://svnweb.freebsd.org/changeset/ports/316940 Log: - Update to 1.13.0 - Improve COMMENT (remove leading article, add missing space) - Remove unneeded BSD license file - Trim Makefile's header - Pet portlint (move LICENSE section earlier, change tab to space in WWW link) Changes: http://sourceforge.net/p/staden/news/2013/03/iolib-1130-released/ Added: head/biology/iolib/files/ head/biology/iolib/files/patch-progs-scram__merge.c (contents, props changed) head/biology/iolib/files/patch-progs-scramble.c (contents, props changed) Modified: head/biology/iolib/Makefile (contents, props changed) head/biology/iolib/distinfo (contents, props changed) head/biology/iolib/pkg-descr (contents, props changed) head/biology/iolib/pkg-plist (contents, props changed) Modified: head/biology/iolib/Makefile ============================================================================== --- head/biology/iolib/Makefile Tue Apr 30 15:17:38 2013 (r316939) +++ head/biology/iolib/Makefile Tue Apr 30 15:41:49 2013 (r316940) @@ -1,30 +1,25 @@ -# New ports collection makefile for: io_lib -# Date created: 27 Aug, 2009 -# Whom: Wen Heping <wenheping@gmail.com> -# +# Created by: Wen Heping <wenheping@gmail.com> # $FreeBSD$ -# PORTNAME= io_lib -PORTVERSION= 1.12.5 +PORTVERSION= 1.13.0 CATEGORIES= biology MASTER_SITES= SF MASTER_SITE_SUBDIR= staden/${PORTNAME}/${PORTVERSION} MAINTAINER= culot@FreeBSD.org -COMMENT= A general purpose trace file(and Experiment File) reading interface - -LIB_DEPENDS= curl.6:${PORTSDIR}/ftp/curl +COMMENT= General purpose trace file (and Experiment File) reading interface LICENSE= BSD -LICENSE_FILE= ${WRKSRC}/COPYRIGHT + +LIB_DEPENDS= curl:${PORTSDIR}/ftp/curl USE_AUTOTOOLS= libtool:env GNU_CONFIGURE= yes USE_GMAKE= yes USE_LDCONFIG= yes -MAN1= srf_index_hash.1 srf_info.1 srf_list.1 \ +MAN1= scramble.1 srf_index_hash.1 srf_info.1 srf_list.1 \ srf2fasta.1 srf2fastq.1 MAN3= read_scf_header.3 read_allocate.3 ExperimentFile.3 \ write_reading.3 write_scf.3 read_deallocate.3 \ Modified: head/biology/iolib/distinfo ============================================================================== --- head/biology/iolib/distinfo Tue Apr 30 15:17:38 2013 (r316939) +++ head/biology/iolib/distinfo Tue Apr 30 15:41:49 2013 (r316940) @@ -1,2 +1,2 @@ -SHA256 (io_lib-1.12.5.tar.gz) = 0bcecddaad5e94f1f9d2e9f2ae37e4303b6e8d0c9f6dabecb6bbebd6816fe80f -SIZE (io_lib-1.12.5.tar.gz) = 782430 +SHA256 (io_lib-1.13.0.tar.gz) = c3e0106802bd1a4a41427304944bcf11b7a4dd249cf470454a35d30cde13db5c +SIZE (io_lib-1.13.0.tar.gz) = 1522227 Added: head/biology/iolib/files/patch-progs-scram__merge.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/iolib/files/patch-progs-scram__merge.c Tue Apr 30 15:41:49 2013 (r316940) @@ -0,0 +1,7 @@ +--- progs/scram_merge.c.orig 2013-04-30 08:30:10.000000000 -0400 ++++ progs/scram_merge.c 2013-04-30 08:30:23.000000000 -0400 +@@ -1,3 +1,4 @@ ++#include <unistd.h> + #include <stdio.h> + #include <stdlib.h> + #include <string.h> Added: head/biology/iolib/files/patch-progs-scramble.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/iolib/files/patch-progs-scramble.c Tue Apr 30 15:41:49 2013 (r316940) @@ -0,0 +1,7 @@ +--- progs/scramble.c.orig 2013-04-30 08:28:30.000000000 -0400 ++++ progs/scramble.c 2013-04-30 08:28:43.000000000 -0400 +@@ -1,3 +1,4 @@ ++#include <unistd.h> + #include <stdio.h> + #include <stdlib.h> + #include <string.h> Modified: head/biology/iolib/pkg-descr ============================================================================== --- head/biology/iolib/pkg-descr Tue Apr 30 15:17:38 2013 (r316939) +++ head/biology/iolib/pkg-descr Tue Apr 30 15:41:49 2013 (r316940) @@ -4,4 +4,4 @@ The programmer simply calls the (eg) rea C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. -WWW: http://staden.sourceforge.net/ +WWW: http://staden.sourceforge.net/ Modified: head/biology/iolib/pkg-plist ============================================================================== --- head/biology/iolib/pkg-plist Tue Apr 30 15:17:38 2013 (r316939) +++ head/biology/iolib/pkg-plist Tue Apr 30 15:41:49 2013 (r316940) @@ -2,9 +2,18 @@ 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/compress.h include/io_lib/compression.h +include/io_lib/cram.h +include/io_lib/cram_codecs.h +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_structs.h include/io_lib/deflate_interlaced.h +include/io_lib/dstring.h include/io_lib/error.h include/io_lib/expFileIO.h include/io_lib/fpoint.h @@ -13,26 +22,34 @@ include/io_lib/io_lib_config.h include/io_lib/jenkins_lookup3.h include/io_lib/mFILE.h include/io_lib/mach-io.h +include/io_lib/md5.h include/io_lib/misc.h include/io_lib/open_trace_file.h include/io_lib/os.h include/io_lib/plain.h include/io_lib/pooled_alloc.h +include/io_lib/sam_header.h 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/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 @@ -45,9 +62,13 @@ 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 @@ -62,5 +83,5 @@ bin/ztr_dump lib/libstaden-read.a lib/libstaden-read.la lib/libstaden-read.so -lib/libstaden-read.so.2 +lib/libstaden-read.so.3 @dirrm include/io_lib
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