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 <[email protected]> Mon, 07 Jul 2008 19:09:31 +0900 +http://lists.debian.org/msgid-search/alpine.deb.1.10.0809021033020.13...@wr-linux02 + +In addition, `libstaden-read` is built as a dynamic library in Debian. + + -- Charles Plessy <[email protected]> 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 <[email protected]> Mon, 07 Jul 2008 19:09:31 +0900 - + -- Charles Plessy <[email protected]> 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 <[email protected]> DM-Upload-Allowed: yes Uploaders: Charles Plessy <[email protected]> -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/* _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
