Date: Tue, 22 Apr 2014 02:57:18 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/188863: biology/iolib: Update to version 1.13.5 Message-ID: <20140422025718.3d9e1a5f4f0a88f7189659bc@yahoo.com> Resent-Message-ID: <201404211810.s3LIA3Pl023407@freefall.freebsd.org>
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>Number: 188863
>Category: ports
>Synopsis: biology/iolib: Update to version 1.13.5
>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: Mon Apr 21 18:10:02 UTC 2014
>Closed-Date:
>Last-Modified:
>Originator: KATO Tsuguru
>Release: FreeBSD 8.4-RELEASE-p8 i386
>Organization:
>Environment:
>Description:
- Update to version 1.13.5
New file:
files/patch-progs__scram_flgstat.c
>How-To-Repeat:
>Fix:
diff -urN /usr/ports/biology/iolib/Makefile biology/iolib/Makefile
--- /usr/ports/biology/iolib/Makefile 2014-04-12 16:45:33.000000000 +0900
+++ biology/iolib/Makefile 2014-04-22 00:00:00.000000000 +0900
@@ -2,11 +2,9 @@
# $FreeBSD: head/biology/iolib/Makefile 351071 2014-04-12 07:42:33Z culot $
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
diff -urN /usr/ports/biology/iolib/distinfo biology/iolib/distinfo
--- /usr/ports/biology/iolib/distinfo 2013-11-06 22:05:39.000000000 +0900
+++ biology/iolib/distinfo 2014-04-22 00:00:00.000000000 +0900
@@ -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
diff -urN /usr/ports/biology/iolib/files/patch-progs__scram_flgstat.c biology/iolib/files/patch-progs__scram_flgstat.c
--- /usr/ports/biology/iolib/files/patch-progs__scram_flgstat.c 1970-01-01 09:00:00.000000000 +0900
+++ biology/iolib/files/patch-progs__scram_flgstat.c 2014-04-22 00:00:00.000000000 +0900
@@ -0,0 +1,10 @@
+--- progs/scram_flagstat.c.orig
++++ progs/scram_flagstat.c
+@@ -44,6 +44,7 @@
+ #include <assert.h>
+ #include <ctype.h>
+ #include <errno.h>
++#include <unistd.h>
+
+ #if defined(__MINGW32__)
+ # include <getopt.h>
diff -urN /usr/ports/biology/iolib/pkg-plist biology/iolib/pkg-plist
--- /usr/ports/biology/iolib/pkg-plist 2014-01-21 17:34:34.000000000 +0900
+++ biology/iolib/pkg-plist 2014-04-22 00:00:00.000000000 +0900
@@ -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_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_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
>Release-Note:
>Audit-Trail:
>Unformatted:
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