From owner-freebsd-ports-bugs@FreeBSD.ORG Fri Aug 28 07:43:24 2009 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 2F1F110656EE for ; Fri, 28 Aug 2009 07:43:24 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 0633F8FEED for ; Fri, 28 Aug 2009 07:42:59 +0000 (UTC) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id n7S7gXdA056330 for ; Fri, 28 Aug 2009 07:42:38 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id n7S7gXtw056329; Fri, 28 Aug 2009 07:42:33 GMT (envelope-from gnats) Resent-Date: Fri, 28 Aug 2009 07:42:33 GMT Resent-Message-Id: <200908280742.n7S7gXtw056329@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Wen Heping Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 207D91065A67 for ; Fri, 28 Aug 2009 07:34:12 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [IPv6:2001:4f8:fff6::21]) by mx1.freebsd.org (Postfix) with ESMTP id 156998FC08 for ; Fri, 28 Aug 2009 07:22:33 +0000 (UTC) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.14.3/8.14.3) with ESMTP id n7S7LqvP064999 for ; Fri, 28 Aug 2009 07:22:02 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.14.3/8.14.3/Submit) id n7S7LlvY064984; Fri, 28 Aug 2009 07:21:47 GMT (envelope-from nobody) Message-Id: <200908280721.n7S7LlvY064984@www.freebsd.org> Date: Fri, 28 Aug 2009 07:21:47 GMT From: Wen Heping To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/138262: [NEW PORT]biology/iolib:A general purpose trace file(and Experiment File) reading interface X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 28 Aug 2009 07:43:24 -0000 >Number: 138262 >Category: ports >Synopsis: [NEW PORT]biology/iolib:A general purpose trace file(and Experiment File) reading interface >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Fri Aug 28 07:42:18 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Wen Heping >Release: FreeBSD 8.0-Current >Organization: ChangAn Middle School >Environment: FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #0: Sun Mar 22 22:12:06 CST 2009 root@fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC i386 >Description: Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" 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/ >How-To-Repeat: >Fix: Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # iolib # iolib/Makefile # iolib/distinfo # iolib/pkg-descr # iolib/pkg-plist # echo c - iolib mkdir -p iolib > /dev/null 2>&1 echo x - iolib/Makefile sed 's/^X//' >iolib/Makefile << 'b7ad3746b47ea4d30cc028e26598a798' X# New ports collection makefile for: io_lib X# Date created: 27 Aug, 2009 X# Whom: Wen Heping X# X# $FreeBSD$ X# X XPORTNAME= io_lib XPORTVERSION= 1.12.1 XCATEGORIES= biology XMASTER_SITES= SF XMASTER_SITE_SUBDIR= staden/${PORTNAME}/${PORTVERSION} X XMAINTAINER= wenheping@gmail.com XCOMMENT= A general purpose trace file(and Experiment File) reading interface X XUSE_AUTOTOOLS= libtool:22:env XGNU_CONFIGURE= yes XUSE_GMAKE= yes XUSE_LDCONFIG= yes X XMAN1= srf_index_hash.1 srf_info.1 srf_list.1 illumina2srf.1 \ X srf2fasta.1 srf2fastq.1 XMAN3= read_scf_header.3 read_allocate.3 ExperimentFile.3 \ X write_reading.3 write_scf.3 read_deallocate.3 \ X fwrite_reading.3 read2scf.3 scf2read.3 \ X fwrite_scf.3 write_scf_header.3 read_reading.3 \ X read_scf.3 exp2read.3 fread_reading.3 \ X read2exp.3 fread_scf.3 XMAN4= Read.4 X X.include b7ad3746b47ea4d30cc028e26598a798 echo x - iolib/distinfo sed 's/^X//' >iolib/distinfo << '6ece5bfd27be348ff9fef9c9bb26bcaf' XMD5 (io_lib-1.12.1.tar.gz) = f511698b766d5bd7d15a8269bdcddf84 XSHA256 (io_lib-1.12.1.tar.gz) = 732fc729662f380861e12fd9006a1a1c072f459589b6d2c49a7c01c88a9cdf01 XSIZE (io_lib-1.12.1.tar.gz) = 772314 6ece5bfd27be348ff9fef9c9bb26bcaf echo x - iolib/pkg-descr sed 's/^X//' >iolib/pkg-descr << 'c04402d888d8b1769b87fa52eff5c855' XIo_lib is a library of file reading and writing code to provide a Xgeneral purpose trace file (and Experiment File) reading interface. XThe programmer simply calls the (eg) read_reading to create a "Read" XC structure with the data loaded into memory. It has been compiled Xand tested on a variety of unix systems, MacOS X and MS Windows. X XWWW: http://staden.sourceforge.net/ c04402d888d8b1769b87fa52eff5c855 echo x - iolib/pkg-plist sed 's/^X//' >iolib/pkg-plist << '0298aa480c8dd33592e6b51a7423979d' Xinclude/io_lib/Read.h Xinclude/io_lib/abi.h Xinclude/io_lib/alf.h Xinclude/io_lib/array.h Xinclude/io_lib/compress.h Xinclude/io_lib/compression.h Xinclude/io_lib/deflate_interlaced.h Xinclude/io_lib/error.h Xinclude/io_lib/expFileIO.h Xinclude/io_lib/fpoint.h Xinclude/io_lib/hash_table.h Xinclude/io_lib/io_lib_config.h Xinclude/io_lib/jenkins_lookup3.h Xinclude/io_lib/mFILE.h Xinclude/io_lib/mach-io.h Xinclude/io_lib/misc.h Xinclude/io_lib/open_trace_file.h Xinclude/io_lib/os.h Xinclude/io_lib/plain.h Xinclude/io_lib/scf.h Xinclude/io_lib/scf_extras.h Xinclude/io_lib/seqIOABI.h Xinclude/io_lib/seqIOCTF.h Xinclude/io_lib/sff.h Xinclude/io_lib/srf.h Xinclude/io_lib/stdio_hack.h Xinclude/io_lib/tar_format.h Xinclude/io_lib/traceType.h Xinclude/io_lib/translate.h Xinclude/io_lib/vlen.h Xinclude/io_lib/xalloc.h Xinclude/io_lib/ztr.h Xbin/append_sff Xbin/convert_trace Xbin/extract_fastq Xbin/extract_qual Xbin/extract_seq Xbin/get_comment Xbin/hash_extract Xbin/hash_list Xbin/hash_sff Xbin/hash_tar Xbin/index_tar Xbin/io_lib-config Xbin/makeSCF Xbin/scf_dump Xbin/scf_info Xbin/scf_update Xbin/srf2fasta Xbin/srf2fastq Xbin/srf_dump_all Xbin/srf_extract_hash Xbin/srf_extract_linear Xbin/srf_filter Xbin/srf_index_hash Xbin/srf_info Xbin/srf_list Xbin/trace_dump Xbin/ztr_dump Xlib/libstaden-read.a Xlib/libstaden-read.la Xlib/libstaden-read.so Xlib/libstaden-read.so.1 X@dirrm include/io_lib 0298aa480c8dd33592e6b51a7423979d exit >Release-Note: >Audit-Trail: >Unformatted: