[med-svn] r21401 - trunk/packages/tantan/trunk/debian

Sascha Steinbiss sascha-guest at moszumanska.debian.org
Mon Feb 15 23:56:19 UTC 2016 

Author: sascha-guest
Date: 2016-02-15 23:56:19 +0000 (Mon, 15 Feb 2016)
New Revision: 21401

Added:
   trunk/packages/tantan/trunk/debian/README.status
Removed:
   trunk/packages/tantan/trunk/debian/changelog
   trunk/packages/tantan/trunk/debian/compat
   trunk/packages/tantan/trunk/debian/control
   trunk/packages/tantan/trunk/debian/copyright
   trunk/packages/tantan/trunk/debian/createmanpages
   trunk/packages/tantan/trunk/debian/lintian-overrides
   trunk/packages/tantan/trunk/debian/manpages
   trunk/packages/tantan/trunk/debian/rules
   trunk/packages/tantan/trunk/debian/source/
   trunk/packages/tantan/trunk/debian/tantan.1
   trunk/packages/tantan/trunk/debian/upstream/
   trunk/packages/tantan/trunk/debian/watch
Log:
migrate to Git


Added: trunk/packages/tantan/trunk/debian/README.status
===================================================================
--- trunk/packages/tantan/trunk/debian/README.status	                        (rev 0)
+++ trunk/packages/tantan/trunk/debian/README.status	2016-02-15 23:56:19 UTC (rev 21401)
@@ -0,0 +1 @@
+This package has been migrated to Git: https://anonscm.debian.org/git/debian-med/tantan.git

Deleted: trunk/packages/tantan/trunk/debian/changelog
===================================================================
--- trunk/packages/tantan/trunk/debian/changelog	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/changelog	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1,7 +0,0 @@
-tantan (13-1) unstable; urgency=low
-
-  * Initial release (Closes: #793907)
-  * Add missing copyright holder in d/copyright
-  * Fix machine readable license code
-
- -- Sascha Steinbiss <sascha at steinbiss.name>  Tue, 04 Aug 2015 23:24:50 +0000

Deleted: trunk/packages/tantan/trunk/debian/compat
===================================================================
--- trunk/packages/tantan/trunk/debian/compat	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/compat	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1 +0,0 @@
-9

Deleted: trunk/packages/tantan/trunk/debian/control
===================================================================
--- trunk/packages/tantan/trunk/debian/control	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/control	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1,20 +0,0 @@
-Source: tantan
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Sascha Steinbiss <sascha at steinbiss.name>
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.6
-Homepage: http://www.cbrc.jp/tantan/
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/tantan/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/tantan/trunk/
-
-Package: tantan
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: low complexity and tandem repeat masker for biosequences
- tantan is a tool to mask simple regions (low complexity and short-period tandem
- repeats) in DNA, RNA, and protein sequences. The aim of tantan is to prevent
- false predictions when searching for homologous regions between two sequences.
- Simple repeats often align strongly to each other, causing false homology
- predictions.
\ No newline at end of file

Deleted: trunk/packages/tantan/trunk/debian/copyright
===================================================================
--- trunk/packages/tantan/trunk/debian/copyright	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/copyright	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1,31 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: tantan
-Source: http://www.cbrc.jp/tantan/
-
-Files: *
-Copyright: © 2010 Martin Frith <tantan at cbrc.jp>
-           © 2008 Michiaki Hamada <mhamada at waseda.jp>
-           © Stephen Altschul <altschul at ncbi.nlm.nih.gov>
-           © Yi-Kuo Yu <yyu at ncbi.nlm.nih.gov>
-License: GPL-3+
-
-Files: debian/*
-Copyright: © 2015 Sascha Steinbiss <sascha at steinbiss.name>
-License: GPL-3+
-
-License: GPL-3+
- This program 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 3 of the License, or
- (at your option) any later version.
- .
- This program 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 program.  If not, see <http://www.gnu.org/licenses/>.
- .
- On Debian Systems you can find a copy of the text of GPL version 3
- at /usr/share/common-licenses/GPL-3.

Deleted: trunk/packages/tantan/trunk/debian/createmanpages
===================================================================
--- trunk/packages/tantan/trunk/debian/createmanpages	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/createmanpages	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1,16 +0,0 @@
-#!/bin/sh
-MANDIR=debian
-mkdir -p $MANDIR
-
-VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
-
-help2man --no-info --no-discard-stderr --help-option="-h" \
-         --name='low complexity and tandem repeat masker for biosequences' \
-            --version-string="$VERSION" tantan > $MANDIR/tantan.1
-
-cat <<EOT
-Please enhance the help2man output.
-The following web page might be helpful in doing so:
-    http://liw.fi/manpages/
-EOT
-

Deleted: trunk/packages/tantan/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/tantan/trunk/debian/lintian-overrides	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/lintian-overrides	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1 +0,0 @@
-tantan binary: hardening-no-fortify-functions *

Deleted: trunk/packages/tantan/trunk/debian/manpages
===================================================================
--- trunk/packages/tantan/trunk/debian/manpages	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/manpages	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1 +0,0 @@
-debian/tantan.1

Deleted: trunk/packages/tantan/trunk/debian/rules
===================================================================
--- trunk/packages/tantan/trunk/debian/rules	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/rules	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1,16 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-export DESTDIR=$(CURDIR)/debian/tantan/usr
-export DH_ALWAYS_EXCLUDE=.gitignore
-
-CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
-CFLAGS:=$(shell dpkg-buildflags --get CFLAGS)
-CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS)
-LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
-
-%:
-	dh $@
-
-override_dh_auto_install:
-	make prefix=$(DESTDIR) install

Deleted: trunk/packages/tantan/trunk/debian/tantan.1
===================================================================
--- trunk/packages/tantan/trunk/debian/tantan.1	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/tantan.1	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1,58 +0,0 @@
-.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
-.TH TANTAN "1" "July 2015" "tantan 13" "User Commands"
-.SH NAME
-tantan \- low complexity and tandem repeat masker for biosequences
-.SH SYNOPSIS
-.B tantan
-[\fI\,options\/\fR] \fI\,fasta-sequence-file(s)\/\fR
-.SH DESCRIPTION
-Find simple repeats in sequences
-.SS "Options (default settings):"
-.TP
-\fB\-p\fR
-interpret the sequences as proteins
-.TP
-\fB\-x\fR
-letter to use for masking, instead of lowercase
-.TP
-\fB\-c\fR
-preserve uppercase/lowercase in non\-masked regions
-.TP
-\fB\-m\fR
-file for letter pair scores (+1/\-1, but \fB\-p\fR selects BLOSUM62)
-.TP
-\fB\-r\fR
-probability of a repeat starting per position (0.005)
-.TP
-\fB\-e\fR
-probability of a repeat ending per position (0.05)
-.TP
-\fB\-w\fR
-maximum tandem repeat period to consider (100, but \fB\-p\fR selects 50)
-.TP
-\fB\-d\fR
-probability decay per period (0.9)
-.TP
-\fB\-a\fR
-gap existence cost (0)
-.TP
-\fB\-b\fR
-gap extension cost (infinite: no gaps)
-.TP
-\fB\-s\fR
-minimum repeat probability for masking (0.5)
-.TP
-\fB\-f\fR
-output type: 0=masked sequence, 1=repeat probabilities,
-.IP
-2=repeat counts, 3=BED (0)
-.TP
-\fB\-h\fR, \fB\-\-help\fR
-show help message, then exit
-.TP
-\fB\-\-version\fR
-show version information, then exit
-.SH "REPORTING BUGS"
-Report bugs to: tantan at cbrc.jp
-.br
-Home page: http://www.cbrc.jp/tantan/

Deleted: trunk/packages/tantan/trunk/debian/watch
===================================================================
--- trunk/packages/tantan/trunk/debian/watch	2016-02-15 19:27:48 UTC (rev 21400)
+++ trunk/packages/tantan/trunk/debian/watch	2016-02-15 23:56:19 UTC (rev 21401)
@@ -1,2 +0,0 @@
-version=3
-http://cbrc3.cbrc.jp/~martin/tantan/tantan-([0-9]*).zip

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