[med-svn] r3445 - in trunk/packages/staden-io-lib/trunk/debian: . patches

Charles Plessy plessy at alioth.debian.org
Fri May 29 05:26:09 UTC 2009 

Author: plessy
Date: 2009-05-29 05:26:09 +0000 (Fri, 29 May 2009)
New Revision: 3445

Added:
   trunk/packages/staden-io-lib/trunk/debian/libstaden-read-dev.manpages
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.doc-base.staden-io-lib-hash-file-format
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.doc-base.staden-io-lib-ztr-format
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.docs
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.install
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.manpages
Removed:
   trunk/packages/staden-io-lib/trunk/debian/docs
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.doc-base.staden-io-lib_ZTR_format
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.install
Modified:
   trunk/packages/staden-io-lib/trunk/debian/README.Debian
   trunk/packages/staden-io-lib/trunk/debian/changelog
   trunk/packages/staden-io-lib/trunk/debian/control
   trunk/packages/staden-io-lib/trunk/debian/patches/libtoolization-and-renaming.patch
   trunk/packages/staden-io-lib/trunk/debian/rules
Log:
Uploaded a ~rc1 version, for comments on sonames. Other changes are mostly about documentation.


Modified: trunk/packages/staden-io-lib/trunk/debian/README.Debian
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/README.Debian	2009-05-28 22:19:30 UTC (rev 3444)
+++ trunk/packages/staden-io-lib/trunk/debian/README.Debian	2009-05-29 05:26:09 UTC (rev 3445)
@@ -1,7 +1,12 @@
-staden-io-lib for Debian
--------------------------
+Staden packages’s io_lib for Debian
+-----------------------------------
 
-This package is unofficial and builds dynamic libraries using a patch that is
-not yet accepted upstream.
+After discussion with the maintainer of the io_lib, the `libread` was renamed
+`libstaden-read` in Debian. The same renaming happened in Fedora and the change
+may be propagated upstream. See our archived discussion:
 
- -- Charles Plessy <plessy at debian.org>  Mon, 07 Jul 2008 19:09:31 +0900
+http://lists.debian.org/msgid-search/alpine.DEB.1.10.0809021033020.13723@wr-linux02
+
+In addition, `libstaden-read` is built as a dynamic library in Debian.
+
+ -- Charles Plessy <plessy at debian.org>  Fri, 29 May 2009 13:26:03 +0900

Modified: trunk/packages/staden-io-lib/trunk/debian/changelog
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/changelog	2009-05-28 22:19:30 UTC (rev 3444)
+++ trunk/packages/staden-io-lib/trunk/debian/changelog	2009-05-29 05:26:09 UTC (rev 3445)
@@ -1,6 +1,5 @@
-staden-io-lib (1.11.6.1-1) UNRELEASED; urgency=low
+staden-io-lib (1.11.6.1-1~rc1) for-review; urgency=low
 
   * Initial release (Closes: #530753)
 
- -- Charles Plessy <plessy at debian.org>  Mon, 07 Jul 2008 19:09:31 +0900
-
+ -- Charles Plessy <plessy at debian.org>  Fri, 29 May 2009 13:26:38 +0900

Modified: trunk/packages/staden-io-lib/trunk/debian/control
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/control	2009-05-28 22:19:30 UTC (rev 3444)
+++ trunk/packages/staden-io-lib/trunk/debian/control	2009-05-29 05:26:09 UTC (rev 3445)
@@ -4,14 +4,16 @@
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Charles Plessy <plessy at debian.org>
-Build-Depends: debhelper (>= 7), autotools-dev, quilt
+Build-Depends:
+ debhelper (>= 7), quilt,
+ autotools-dev, automake, autoconf, libtool,
+ zlib1g-dev
 Standards-Version: 3.8.1
 Homepage: http://staden.sourceforge.net/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/staden-io-lib/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/staden-io-lib/trunk/
 
 Package: staden-io-lib-utils
-Section: science
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: programs for maniuplating DNA sequencing files
@@ -32,12 +34,22 @@
 Description: development files for libstaden-read
  This package contains the header and development files needed to build
  programs and packages using the Staden io_lib.
+ .
+ The io_lib from the Staden package is a library of file reading and writing
+ code to provide a general purpose trace file (and Experiment File) reading
+ interface. It has been compiled and tested on a variety of unix systems,
+ MacOS X and MS Windows.
 
 Package: libstaden-read1
 Section: libs
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: Staden library for reading and writing DNA sequencing results.
- This package contains the Staden io_lib, that is renamed in Debian and Fedora
- ‘staden-read’ instead of ‘read’. This library supports various DNA sequence
- read formats, in particular SCF, ABI, ALF, CTF, ZTR, SFF and SRF.
+Description: Staden library for reading and writing DNA sequencing results
+ This package contains the Staden io_lib, that is renamed in Debian and
+ Fedora ‘staden-read’ instead of ‘read’. This library supports various DNA
+ sequence read formats, in particular SCF, ABI, ALF, CTF, ZTR, SFF and SRF.
+ .
+ The io_lib from the Staden package is a library of file reading and writing
+ code to provide a general purpose trace file (and Experiment File) reading
+ interface. It has been compiled and tested on a variety of unix systems,
+ MacOS X and MS Windows.

Deleted: trunk/packages/staden-io-lib/trunk/debian/docs
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/docs	2009-05-28 22:19:30 UTC (rev 3444)
+++ trunk/packages/staden-io-lib/trunk/debian/docs	2009-05-29 05:26:09 UTC (rev 3445)
@@ -1,4 +0,0 @@
-README
-CHANGES
-docs/Hash_File_Format
-docs/ZTR_format

Added: trunk/packages/staden-io-lib/trunk/debian/libstaden-read-dev.manpages
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/libstaden-read-dev.manpages	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/libstaden-read-dev.manpages	2009-05-29 05:26:09 UTC (rev 3445)
@@ -0,0 +1,2 @@
+man/man3/*3
+man/man4/*4

Modified: trunk/packages/staden-io-lib/trunk/debian/patches/libtoolization-and-renaming.patch
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/patches/libtoolization-and-renaming.patch	2009-05-28 22:19:30 UTC (rev 3444)
+++ trunk/packages/staden-io-lib/trunk/debian/patches/libtoolization-and-renaming.patch	2009-05-29 05:26:09 UTC (rev 3445)
@@ -2,11 +2,9 @@
 Description: renames `libread' `libstaden-read', and implements libtool.
 Forwarded: https://sourceforge.net/tracker/?func=detail&aid=2082376&group_id=100316&atid=627060
 License: same as the io_lib itself.
-diff --git a/configure.in b/configure.in
-index dab45b5..fffd268 100644
---- a/configure.in
-+++ b/configure.in
-@@ -7,7 +7,7 @@ AM_MAINTAINER_MODE
+--- io_lib-1.11.6.orig/configure.in
++++ io_lib-1.11.6/configure.in
+@@ -7,7 +7,7 @@
  dnl Checks for programs.
  AC_PROG_CC
  AC_PROG_INSTALL
@@ -15,10 +13,8 @@
  
  dnl Check for libcurl and zlib
  LIBCURL_CHECK_CONFIG(,,[have_curl=yes], [have_curl=no])
-diff --git a/io_lib/Makefile.am b/io_lib/Makefile.am
-index c10175f..4a270e9 100644
---- a/io_lib/Makefile.am
-+++ b/io_lib/Makefile.am
+--- io_lib-1.11.6.orig/io_lib/Makefile.am
++++ io_lib-1.11.6/io_lib/Makefile.am
 @@ -1,6 +1,6 @@
 -lib_LIBRARIES = libread.a
 +lib_LTLIBRARIES = libstaden-read.la
@@ -28,7 +24,7 @@
  	Read.c \
  	Read.h \
  	scf_extras.c \
-@@ -67,8 +67,8 @@ libread_a_SOURCES = \
+@@ -67,8 +67,8 @@
  	os.h \
  	stdio_hack.h
  
@@ -39,10 +35,8 @@
 +#libstaden-read_la_LDFLAGS = -avoid-version
  
  INCLUDES = -I${top_srcdir}
-diff --git a/progs/Makefile.am b/progs/Makefile.am
-index 4744daa..2b1660a 100644
---- a/progs/Makefile.am
-+++ b/progs/Makefile.am
+--- io_lib-1.11.6.orig/progs/Makefile.am
++++ io_lib-1.11.6/progs/Makefile.am
 @@ -1,86 +1,86 @@
  bin_PROGRAMS = convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump illumina2srf srf2illumina srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list
  
@@ -157,3 +151,14 @@
 +srf_list_LDADD = -L$(top_builddir)/io_lib/.libs -lstaden-read @LIBZ@ @LIBCURL@
  
  INCLUDES= -I${top_srcdir}
+--- io_lib-1.11.6.orig/bootstrap
++++ io_lib-1.11.6/bootstrap
+@@ -4,7 +4,7 @@
+ 
+ set -x
+ rm -rf install-sh missing mkinstalldirs depcomp aclocal.m4 config.cache config.log config.status configure autom4te.cache io_lib_config.h.in config.sub config.guess Makefile.in progs/Makefile.in progs/Makefile read/Makefile.in read/Makefile tests/Makefile tests/Makefile.in dependencies io_lib-config
+-#libtoolize --force --copy && \
++libtoolize --force --copy && \
+ aclocal -I . && \
+ autoheader && \
+ automake --foreign --add-missing --copy && \

Modified: trunk/packages/staden-io-lib/trunk/debian/rules
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/rules	2009-05-28 22:19:30 UTC (rev 3444)
+++ trunk/packages/staden-io-lib/trunk/debian/rules	2009-05-29 05:26:09 UTC (rev 3445)
@@ -12,16 +12,6 @@
 CROSS= --build $(DEB_BUILD_GNU_TYPE)
 endif
 
-
-# shared library versions, option 1
-version=1.11.6
-major=1
-# option 2, assuming the library is created as src/.libs/libfoo.so.2.0.5 or so
-#version=`ls src/.libs/lib*.so.* | \
-# awk '{if (match($$0,/[0-9]+\.[0-9]+\.[0-9]+$$/)) print substr($$0,RSTART)}'`
-#major=`ls src/.libs/lib*.so.* | \
-# awk '{if (match($$0,/\.so\.[0-9]+$$/)) print substr($$0,RSTART+4)}'`
-
 config.status: configure
 	./bootstrap
 	dh_testdir
@@ -31,10 +21,9 @@
 ifneq "$(wildcard /usr/share/misc/config.guess)" ""
 	cp --remove-destination /usr/share/misc/config.guess config.guess
 endif
-	#./configure $(CROSS) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info CFLAGS="$(CFLAGS) -Os" LDFLAGS="-Wl,-z,defs"
 	./configure $(CROSS) --prefix=/usr --mandir=\$${prefix}/share/man --infodir=\$${prefix}/share/info 
 
-build: build-stamp
+build: patch build-stamp
 build-stamp: config.status 
 	dh build
 

Added: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.doc-base.staden-io-lib-hash-file-format
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.doc-base.staden-io-lib-hash-file-format	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.doc-base.staden-io-lib-hash-file-format	2009-05-29 05:26:09 UTC (rev 3445)
@@ -0,0 +1,8 @@
+Document: staden-io-lib-hash-file-format
+Title: Hash_File_Format specification.
+Author: <insert document author here>
+Abstract: This document specifies the Hash_File_Format format for biological sequences.
+Section: Science/Biology
+
+Format: text
+Files: /usr/share/doc/staden-io-lib-utils/Hash_File_Format

Copied: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.doc-base.staden-io-lib-ztr-format (from rev 3444, trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.doc-base.staden-io-lib_ZTR_format)
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.doc-base.staden-io-lib-ztr-format	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.doc-base.staden-io-lib-ztr-format	2009-05-29 05:26:09 UTC (rev 3445)
@@ -0,0 +1,9 @@
+Document: staden-io-lib-ztr-format
+Title: ZTR format specification version 1.3
+Author: <insert document author here>
+Abstract: This document specifies the ZTR 1.3 format for biological sequences
+ and discusses the possibles changes towards a 2.0 format.
+Section: Science/Biology
+
+Format: text
+Files: /usr/share/doc/staden-io-lib-utils/ZTR_format.gz

Copied: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.docs (from rev 3444, trunk/packages/staden-io-lib/trunk/debian/docs)
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.docs	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.docs	2009-05-29 05:26:09 UTC (rev 3445)
@@ -0,0 +1,4 @@
+README
+CHANGES
+docs/Hash_File_Format
+docs/ZTR_format


Property changes on: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.docs
___________________________________________________________________
Added: svn:mergeinfo
   + 

Copied: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.install (from rev 3444, trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.install)
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.install	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.install	2009-05-29 05:26:09 UTC (rev 3445)
@@ -0,0 +1 @@
+usr/bin/*


Property changes on: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.install
___________________________________________________________________
Added: svn:mergeinfo
   + 

Added: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.manpages
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.manpages	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-utils.manpages	2009-05-29 05:26:09 UTC (rev 3445)
@@ -0,0 +1 @@
+man/man1/*1

Deleted: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.doc-base.staden-io-lib_ZTR_format
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.doc-base.staden-io-lib_ZTR_format	2009-05-28 22:19:30 UTC (rev 3444)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.doc-base.staden-io-lib_ZTR_format	2009-05-29 05:26:09 UTC (rev 3445)
@@ -1,9 +0,0 @@
-Document: io-lib_ZTR_format
-Title: ZTR format specification version 1.3
-Author: <insert document author here>
-Abstract: This document specifies the ZTR 1.3 format for biological sequences
- and discusses the possibles changes towards a 2.0 format.
-Section: Applications/Science/Biology
-
-Format: text
-Files: /usr/share/doc/io-lib/ZTR_format.gz

Deleted: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.install
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.install	2009-05-28 22:19:30 UTC (rev 3444)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib.install	2009-05-29 05:26:09 UTC (rev 3445)
@@ -1 +0,0 @@
-usr/bin/*

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