Bug 188863 - biology/iolib: Update to version 1.13.5
Summary: biology/iolib: Update to version 1.13.5
Status: Closed FIXED
Alias: None
Product: Ports & Packages
Classification: Unclassified
Component: Individual Port(s) (show other bugs)
Version: Latest
Hardware: Any Any
: Normal Affects Only Me
Assignee: Martin Wilke
URL:
Keywords:
Depends on:
Blocks:
 
Reported: 2014-04-21 19:10 UTC by tkato432
Modified: 2014-04-26 03:40 UTC (History)
0 users

See Also:


Attachments
file.diff (4.01 KB, patch)
2014-04-21 19:10 UTC, tkato432
no flags Details | Diff

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Description tkato432 2014-04-21 19:10:02 UTC
- Update to version 1.13.5 

New file:
files/patch-progs__scram_flgstat.c
Comment 1 Edwin Groothuis freebsd_committer 2014-04-21 19:10:17 UTC
Responsible Changed
From-To: freebsd-ports-bugs->miwi

miwi@ wants this submitter's PRs (via the GNATS Auto Assign Tool)
Comment 2 Martin Wilke freebsd_committer 2014-04-26 03:35:29 UTC
State Changed
From-To: open->closed

Committed. Thanks!
Comment 3 dfilter service freebsd_committer 2014-04-26 03:35:44 UTC
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 <assert.h>
+ #include <ctype.h>
+ #include <errno.h>
++#include <unistd.h>
+ 
+ #if defined(__MINGW32__)
+ #   include <getopt.h>

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
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