[med-svn] r9189 - in trunk/packages/mira/tags: . 3.4.0.1-2/debian
Charles Plessy
plessy at alioth.debian.org
Sat Jan 7 04:53:36 UTC 2012
Author: plessy
Date: 2012-01-07 04:53:35 +0000 (Sat, 07 Jan 2012)
New Revision: 9189
Added:
trunk/packages/mira/tags/3.4.0.1-2/
trunk/packages/mira/tags/3.4.0.1-2/debian/changelog
trunk/packages/mira/tags/3.4.0.1-2/debian/control
trunk/packages/mira/tags/3.4.0.1-2/debian/copyright
Removed:
trunk/packages/mira/tags/3.4.0.1-2/debian/changelog
trunk/packages/mira/tags/3.4.0.1-2/debian/control
trunk/packages/mira/tags/3.4.0.1-2/debian/copyright
Log:
[svn-buildpackage] Tagging mira 3.4.0.1-2
Deleted: trunk/packages/mira/tags/3.4.0.1-2/debian/changelog
===================================================================
--- trunk/packages/mira/trunk/debian/changelog 2012-01-06 22:28:28 UTC (rev 9184)
+++ trunk/packages/mira/tags/3.4.0.1-2/debian/changelog 2012-01-07 04:53:35 UTC (rev 9189)
@@ -1,84 +0,0 @@
-mira (3.4.0.1-2) UNRELEASED; urgency=low
-
- * Remove two patches:
- - read_default_constructor.patch which introduces a duplicate
- bposhashstat_t() definition
- - fix_duplicate_bposhashstat_t_definition.patch which removes
- this duplicate afterwards
-
- -- Andreas Tille <tille at debian.org> Fri, 09 Dec 2011 09:05:53 +0100
-
-mira (3.4.0.1-1) unstable; urgency=low
-
- * New upstream version
- Closes: #648762 (at least if I'm not missleaded - feel free to reopen)
- * debian/control:
- - Added myself to Uploaders
- - Depends: libtcmalloc-minimal0 [i386 amd64]
- Thanks for the patch to Michael Terry <michael.terry at canonical.com>
- however I left out powerpc where libtcmalloc-minimal0 is not
- available
- Closes: #649093
- - Fixed Vcs fields
- * debian/patches/fix_duplicate_bposhashstat_t_definition.patch
- Remove duplicate defintion of bposhashstat_t()
-
- -- Andreas Tille <tille at debian.org> Thu, 08 Dec 2011 08:50:19 +0100
-
-mira (3.4.0-3ubuntu1) lucid; urgency=low
-
- * Small fix to dependencies - there is no "mira" binary package
-
- -- Tim Booth <tbooth at ceh.ac.uk> Fri, 02 Dec 2011 15:00:35 +0000
-
-mira (3.4.0-3) unstable; urgency=low
-
- * Rendering Tim's additions available for Debian
-
- -- Steffen Moeller <moeller at debian.org> Sat, 03 Sep 2011 01:02:10 +0200
-
-mira (3.4.0-2ubuntu5) lucid; urgency=low
-
- * Small fix to clean target and suppress warnings
- on Lucid backport.
- * Fixed missing dependency which caused misleading configure
- failure.
- * Yet another missing build dep - flex and xxd
-
- -- Tim Booth <tbooth at ceh.ac.uk> Tue, 30 Aug 2011 17:17:11 +0100
-
-mira (3.4.0-2) unstable; urgency=low
-
- * Fixing source tree (removed PDF with no source)
-
- -- Steffen Moeller <moeller at debian.org> Mon, 29 Aug 2011 22:54:53 +0200
-
-mira (3.4.0-1) UNRELEASED; urgency=low
-
- * New upstream version.
- - added default constructor to avoid FTBFS
- * Sposoring Tim's work for Debian
- * Using 3.0 (quilt) source format for bz2 upstream
-
- -- Steffen Moeller <moeller at debian.org> Tue, 23 Aug 2011 20:46:32 +0200
-
-mira (3.4rc3-2) lucid; urgency=low
-
- * Version 3.2.1.8 has been removed from SF.net. Packaging the
- latest RC instead.
- * Fixed linking against tcmalloc (see README)
- * Fixed build of docs - HTML is installed in mira-doc
-
- -- Tim Booth <tbooth at ceh.ac.uk> Fri, 19 Aug 2011 12:35:12 +0100
-
-mira (3.2.1.8-1) UNRELEASED; urgency=low
-
- * Initial release (Closes: #435915)
-
- -- Steffen Moeller <moeller at debian.org> Fri, 04 Mar 2011 11:55:25 +0100
-
-mira (3~rc2-1) UNRELEASED; urgency=low
-
- * Initial packaging.
-
- -- Charles Plessy <plessy at debian.org> Tue, 08 Sep 2009 13:35:31 +0900
Copied: trunk/packages/mira/tags/3.4.0.1-2/debian/changelog (from rev 9188, trunk/packages/mira/trunk/debian/changelog)
===================================================================
--- trunk/packages/mira/tags/3.4.0.1-2/debian/changelog (rev 0)
+++ trunk/packages/mira/tags/3.4.0.1-2/debian/changelog 2012-01-07 04:53:35 UTC (rev 9189)
@@ -0,0 +1,90 @@
+mira (3.4.0.1-2) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * Remove two patches:
+ - read_default_constructor.patch which introduces a duplicate
+ bposhashstat_t() definition
+ - fix_duplicate_bposhashstat_t_definition.patch which removes
+ this duplicate afterwards
+
+ [ Charles Plessy ]
+ * Removed unconditional dependency on libtcmalloc-minimal0 (debian/control).
+ Closes: #654884
+ * Machine-readable debian/copyright file.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 07 Jan 2012 13:24:48 +0900
+
+mira (3.4.0.1-1) unstable; urgency=low
+
+ * New upstream version
+ Closes: #648762 (at least if I'm not mislead - feel free to reopen)
+ * debian/control:
+ - Added myself to Uploaders
+ - Depends: libtcmalloc-minimal0 [i386 amd64]
+ Thanks for the patch to Michael Terry <michael.terry at canonical.com>
+ however I left out powerpc where libtcmalloc-minimal0 is not
+ available
+ Closes: #649093
+ - Fixed Vcs fields
+ * debian/patches/fix_duplicate_bposhashstat_t_definition.patch
+ Remove duplicate definition of bposhashstat_t()
+
+ -- Andreas Tille <tille at debian.org> Thu, 08 Dec 2011 08:50:19 +0100
+
+mira (3.4.0-3ubuntu1) lucid; urgency=low
+
+ * Small fix to dependencies - there is no "mira" binary package
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 02 Dec 2011 15:00:35 +0000
+
+mira (3.4.0-3) unstable; urgency=low
+
+ * Rendering Tim's additions available for Debian
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 03 Sep 2011 01:02:10 +0200
+
+mira (3.4.0-2ubuntu5) lucid; urgency=low
+
+ * Small fix to clean target and suppress warnings
+ on Lucid backport.
+ * Fixed missing dependency which caused misleading configure
+ failure.
+ * Yet another missing build dep - flex and xxd
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 30 Aug 2011 17:17:11 +0100
+
+mira (3.4.0-2) unstable; urgency=low
+
+ * Fixing source tree (removed PDF with no source)
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 29 Aug 2011 22:54:53 +0200
+
+mira (3.4.0-1) UNRELEASED; urgency=low
+
+ * New upstream version.
+ - added default constructor to avoid FTBFS
+ * Sponsoring Tim's work for Debian
+ * Using 3.0 (quilt) source format for bz2 upstream
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 23 Aug 2011 20:46:32 +0200
+
+mira (3.4rc3-2) lucid; urgency=low
+
+ * Version 3.2.1.8 has been removed from SF.net. Packaging the
+ latest RC instead.
+ * Fixed linking against tcmalloc (see README)
+ * Fixed build of docs - HTML is installed in mira-doc
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 19 Aug 2011 12:35:12 +0100
+
+mira (3.2.1.8-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #435915)
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 04 Mar 2011 11:55:25 +0100
+
+mira (3~rc2-1) UNRELEASED; urgency=low
+
+ * Initial packaging.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 08 Sep 2009 13:35:31 +0900
Deleted: trunk/packages/mira/tags/3.4.0.1-2/debian/control
===================================================================
--- trunk/packages/mira/trunk/debian/control 2012-01-06 22:28:28 UTC (rev 9184)
+++ trunk/packages/mira/tags/3.4.0.1-2/debian/control 2012-01-07 04:53:35 UTC (rev 9189)
@@ -1,72 +0,0 @@
-Source: mira
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>, Steffen Moeller <moeller at debian.org>,
- Tim Booth <tbooth at ceh.ac.uk>, Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 7.0.50~), autotools-dev, dblatex, docbook-xsl,
- libboost-thread-dev, libboost-regex-dev, libexpat1-dev,
- libtcmalloc-minimal0 [i386 amd64], perl, quilt (>= 0.46-7~), flex,
- vim-common, zlib1g-dev
-Standards-Version: 3.9.2
-Homepage: http://chevreux.org/projects_mira.html
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/
-
-Package: mira-assembler
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, libtcmalloc-minimal0
-Suggests: mira-examples, mira-doc
-Description: Whole Genome Shotgun and EST Sequence Assembler
- The mira genome fragment assembler is a specialised assembler for
- sequencing projects classified as 'hard' due to high number of similar
- repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
- specialised on reconstructing pristine mRNA transcripts while
- detecting and classifying single nucleotide polymorphisms (SNP)
- occuring in different variations thereof.
- .
- The assembler is routinely used for such various tasks as mutation
- detection in different cell types, similarity analysis of transcripts
- between organisms, and pristine assembly of sequences from various
- sources for oligo design in clinical microarray experiments.
- .
- The package provides the following executables:
- Binaries provided:
- * mira: for assembly of genome sequences
- * miramem: estimating memory needed to assemble projects. Realised through
- link to mira.
- * convert_project: for converting project file types into other types
- * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
- frequently used file converters (realised through links to convert_project)
- * scftool: set of tools useful when working with SCF trace files
- * fastatool: set of tools useful when working with FASTA trace files
- .
- Scripts provided:
- * fasta2frag.tcl: fragmenting sequences into smaller, overlapping
- subsequences. Useful for simulating shotgun sequences. Can create
- subsequences in both directions (/default) and also paired-end sequences.
- * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
- a file with names of reads, select the sequences from the input FASTA (and
- quality file) and writes them to an output FASTA
- * fastqselect.tcl: like fastaselect.tcl, only for FASTQ
- * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
- consensus tags in ACE files written by the MIRA assembler (and possibly
- other programs). This script massages an ACE file so that consed can read
- the consensus tags.
-
-
-Package: mira-examples
-Architecture: all
-Depends: ${misc:Depends}
-Suggests: mira-assembler, mira-doc
-Description: files to experiment with the mira assembler
- A series of files to exploit the functionality of mira.
-
-Package: mira-doc
-Section: doc
-Architecture: all
-Depends: ${misc:Depends}
-Suggests: mira-assembler
-Description: documentation for the mira assembler
- An HTML book introducing to mira.
Copied: trunk/packages/mira/tags/3.4.0.1-2/debian/control (from rev 9185, trunk/packages/mira/trunk/debian/control)
===================================================================
--- trunk/packages/mira/tags/3.4.0.1-2/debian/control (rev 0)
+++ trunk/packages/mira/tags/3.4.0.1-2/debian/control 2012-01-07 04:53:35 UTC (rev 9189)
@@ -0,0 +1,72 @@
+Source: mira
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>, Steffen Moeller <moeller at debian.org>,
+ Tim Booth <tbooth at ceh.ac.uk>, Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.0.50~), autotools-dev, dblatex, docbook-xsl,
+ libboost-thread-dev, libboost-regex-dev, libexpat1-dev,
+ libtcmalloc-minimal0 [i386 amd64], perl, quilt (>= 0.46-7~), flex,
+ vim-common, zlib1g-dev
+Standards-Version: 3.9.2
+Homepage: http://chevreux.org/projects_mira.html
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/mira/trunk/
+
+Package: mira-assembler
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: mira-examples, mira-doc
+Description: Whole Genome Shotgun and EST Sequence Assembler
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
+ specialised on reconstructing pristine mRNA transcripts while
+ detecting and classifying single nucleotide polymorphisms (SNP)
+ occuring in different variations thereof.
+ .
+ The assembler is routinely used for such various tasks as mutation
+ detection in different cell types, similarity analysis of transcripts
+ between organisms, and pristine assembly of sequences from various
+ sources for oligo design in clinical microarray experiments.
+ .
+ The package provides the following executables:
+ Binaries provided:
+ * mira: for assembly of genome sequences
+ * miramem: estimating memory needed to assemble projects. Realised through
+ link to mira.
+ * convert_project: for converting project file types into other types
+ * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
+ frequently used file converters (realised through links to convert_project)
+ * scftool: set of tools useful when working with SCF trace files
+ * fastatool: set of tools useful when working with FASTA trace files
+ .
+ Scripts provided:
+ * fasta2frag.tcl: fragmenting sequences into smaller, overlapping
+ subsequences. Useful for simulating shotgun sequences. Can create
+ subsequences in both directions (/default) and also paired-end sequences.
+ * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
+ a file with names of reads, select the sequences from the input FASTA (and
+ quality file) and writes them to an output FASTA
+ * fastqselect.tcl: like fastaselect.tcl, only for FASTQ
+ * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
+ consensus tags in ACE files written by the MIRA assembler (and possibly
+ other programs). This script massages an ACE file so that consed can read
+ the consensus tags.
+
+
+Package: mira-examples
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: mira-assembler, mira-doc
+Description: files to experiment with the mira assembler
+ A series of files to exploit the functionality of mira.
+
+Package: mira-doc
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: mira-assembler
+Description: documentation for the mira assembler
+ An HTML book introducing to mira.
Deleted: trunk/packages/mira/tags/3.4.0.1-2/debian/copyright
===================================================================
--- trunk/packages/mira/trunk/debian/copyright 2012-01-06 22:28:28 UTC (rev 9184)
+++ trunk/packages/mira/tags/3.4.0.1-2/debian/copyright 2012-01-07 04:53:35 UTC (rev 9189)
@@ -1,63 +0,0 @@
-Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-
-Source: http://jaist.dl.sourceforge.net/project/mira-assembler/MIRA/V3rc2/mira-3rc2.tar.bz2
-
-
-© 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas Pfisterer,
-Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecular
-Biophysics.
-© 2001-2007 for MIRA V2.x: Bastien Chevreux.
-
-Author of MIRA
-
-Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches
- Krebsforschungsinstitut, DKFZ) in Heidelberg, DE
- Now at DSM Nutritional Products AG, Kaiseraugst, CH
-
-
-Author of EdIt
-
-Thomas Pfisterer, formerly at the German Cancer Research Center (Deutsches
- Krebsforschungsinstitut, DKFZ) in Heidelberg. DE
- Now at MWG Biotech AG, Ebersberg, DE
-
-
-MIRA, EdIt and accompanying programs of the package are licenced under the GPL
-version 2, both in source code and binaries.
-
-License:
-
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-The file src/io/scf.H uses part of a file from the `Staden package', which is
-released under the following terms:
-
- * Copyright (c) Medical Research Council 1994. All rights reserved.
- *
- * Permission to use, copy, modify and distribute this software and its
- * documentation for any purpose is hereby granted without fee, provided that
- * this copyright and notice appears in all copies.
- *
- * This file was written by James Bonfield, Simon Dear, Rodger Staden,
- * as part of the Staden Package at the MRC Laboratory of Molecular
- * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
- *
- * MRC disclaims all warranties with regard to this software.
-
-The Debian packaging is © 2007, Charles Plessy <charles-debian-nospam at plessy.org> and
-is licensed under as if it were public domain.
Copied: trunk/packages/mira/tags/3.4.0.1-2/debian/copyright (from rev 9187, trunk/packages/mira/trunk/debian/copyright)
===================================================================
--- trunk/packages/mira/tags/3.4.0.1-2/debian/copyright (rev 0)
+++ trunk/packages/mira/tags/3.4.0.1-2/debian/copyright 2012-01-07 04:53:35 UTC (rev 9189)
@@ -0,0 +1,52 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://jaist.dl.sourceforge.net/project/mira-assembler/MIRA/V3rc2/mira-3rc2.tar.bz2
+
+Files: *
+Copyright: © 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas Pfisterer, Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecula Biophysics.
+ © 2001-2007 for MIRA V2.x: Bastien Chevreux.
+License: GPL-2+
+Comment:
+ Author of MIRA
+ .
+ Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches
+ Krebsforschungsinstitut, DKFZ) in Heidelberg, DE
+ Now at DSM Nutritional Products AG, Kaiseraugst, CH
+ .
+ .
+ Author of EdIt
+ .
+ Thomas Pfisterer, formerly at the German Cancer Research Center (Deutsches
+ Krebsforschungsinstitut, DKFZ) in Heidelberg. DE
+ Now at MWG Biotech AG, Ebersberg, DE
+
+Files: src/io/scf.H
+Copyright: © Medical Research Council 1994
+License: staden
+ Permission to use, copy, modify and distribute this software and its
+ documentation for any purpose is hereby granted without fee, provided that
+ this copyright and notice appears in all copies.
+ .
+ This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ as part of the Staden Package at the MRC Laboratory of Molecular
+ Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ .
+ MRC disclaims all warranties with regard to this software.
+Comment: uses part of a file from the `Staden package'.
+
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+Comment: On Debian systems, the complete text of the GNU General Public
+ License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
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