ports/138254: [NEW PORT]biology/iolib:A general purpose trace file(and Experiment File) reading interface

Fri Aug 28 07:36:35 UTC 2009

>Number:         138254
>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 07:30:34 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 at 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 <wenheping at gmail.com>
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 at 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 <bsd.port.mk>
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 at dirrm include/io_lib
0298aa480c8dd33592e6b51a7423979d
exit

>Release-Note:
>Audit-Trail:
>Unformatted: