diff -Nru rate4site-3.0.0/debian/changelog rate4site-3.0.0/debian/changelog --- rate4site-3.0.0/debian/changelog 2013-10-05 19:24:06.000000000 +0000 +++ rate4site-3.0.0/debian/changelog 2016-01-25 08:38:17.000000000 +0000 @@ -1,3 +1,19 @@ +rate4site (3.0.0-2) unstable; urgency=low + + * debian/upstream: Fix syntax + * Moved debian/upstream to debian/upstream/metadata + * Add myself to Uploaders + * debhelper 9 + * Priority: optional + * cme fix dpkg-control + * DEP5 fix + * Remove *-dbg file since this is created automatically + * Cleanup d/rules + * Fix spelling + * Same manpage also for rate4site_doublerep + + -- Andreas Tille Mon, 25 Jan 2016 09:15:42 +0100 + rate4site (3.0.0-1) unstable; urgency=low * Initial release (Closes: #725128). diff -Nru rate4site-3.0.0/debian/compat rate4site-3.0.0/debian/compat --- rate4site-3.0.0/debian/compat 2013-10-01 18:27:52.000000000 +0000 +++ rate4site-3.0.0/debian/compat 2016-01-25 08:07:52.000000000 +0000 @@ -1 +1 @@ -8 +9 diff -Nru rate4site-3.0.0/debian/control rate4site-3.0.0/debian/control --- rate4site-3.0.0/debian/control 2013-10-05 19:23:53.000000000 +0000 +++ rate4site-3.0.0/debian/control 2016-01-25 08:14:47.000000000 +0000 @@ -1,36 +1,26 @@ Source: rate4site -Section: science -Priority: extra Maintainer: Debian Med Packaging Team -Uploaders: Guy Yachdav , Laszlo Kajan -Build-Depends: debhelper (>= 9.0.0), automake, autotools-dev -Standards-Version: 3.9.4 -Homepage: http://www.tau.ac.il/~itaymay/cp/rate4site.html -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/rate4site +Uploaders: Guy Yachdav , + Laszlo Kajan , + Andreas Tille +Section: science +Priority: optional +Build-Depends: debhelper (>= 9), + automake, + autotools-dev +Standards-Version: 3.9.6 +Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/rostlab/rate4site Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/rostlab/rate4site +Homepage: http://www.tau.ac.il/~itaymay/cp/rate4site.html Package: rate4site Architecture: any -Pre-Depends: debconf (>= 0.5) -Depends: ${shlibs:Depends}, ${misc:Depends} -Description: detector of conserved amino-acid sites - Rate4Site calculates the relative evolutionary rate at each site using a - probabilistic-based evolutionary model. - This allows taking into account the stochastic process underlying sequence - evolution within protein families - and the phylogenetic tree of the proteins in the family. - The conservation score at a site corresponds to the site's evolutionary rate. - -Package: rate4site-dbg -Architecture: any -Section: debug -Depends: rate4site (= ${binary:Version}), ${misc:Depends} -Description: debugging symbols for rate4site-dbg - Rate4Site calculates the relative evolutionary rate at each site using a - probabilistic-based evolutionary model. +Depends: ${shlibs:Depends}, + ${misc:Depends} +Description: detector of conserved amino-acid sites + Rate4Site calculates the relative evolutionary rate at each site using a + probabilistic-based evolutionary model. This allows taking into account the stochastic process underlying sequence evolution within protein families - and the phylogenetic tree of the proteins in the family. - The conservation score at a site corresponds to the site's evolutionary rate. - . - This package provides the detached debug symbols for rate4site. + and the phylogenetic tree of the proteins in the family. + The conservation score at a site corresponds to the site's evolutionary rate. diff -Nru rate4site-3.0.0/debian/copyright rate4site-3.0.0/debian/copyright --- rate4site-3.0.0/debian/copyright 2013-10-05 10:15:14.000000000 +0000 +++ rate4site-3.0.0/debian/copyright 2016-01-25 08:13:39.000000000 +0000 @@ -3,6 +3,10 @@ Upstream-Contact: Guy Yachdav Source: ftp://rostlab.org/rate4site/ +Files: * +Copyright: 2013 Nir Ben-Tal +License: GPL-2+ + Files: debian/* Copyright: 2013 Guy Yachdav License: GPL-2+ @@ -11,10 +15,6 @@ Copyright: 1989-1994, 1996-1999, 2001 Free Software Foundation, Inc. License: LGPL-2.1+ -Files: * -Copyright: 2013 Nir Ben-Tal -License: GPL-2+ - License: LGPL-2.1+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public diff -Nru rate4site-3.0.0/debian/links rate4site-3.0.0/debian/links --- rate4site-3.0.0/debian/links 1970-01-01 00:00:00.000000000 +0000 +++ rate4site-3.0.0/debian/links 2016-01-25 08:37:59.000000000 +0000 @@ -0,0 +1 @@ +usr/share/man/man1/rate4site.1.gz usr/share/man/man1/rate4site_doublerep.1.gz diff -Nru rate4site-3.0.0/debian/patches/series rate4site-3.0.0/debian/patches/series --- rate4site-3.0.0/debian/patches/series 2013-10-04 15:14:49.000000000 +0000 +++ rate4site-3.0.0/debian/patches/series 2016-01-25 08:35:39.000000000 +0000 @@ -0,0 +1 @@ +spelling.patch diff -Nru rate4site-3.0.0/debian/patches/spelling.patch rate4site-3.0.0/debian/patches/spelling.patch --- rate4site-3.0.0/debian/patches/spelling.patch 1970-01-01 00:00:00.000000000 +0000 +++ rate4site-3.0.0/debian/patches/spelling.patch 2016-01-25 08:37:11.000000000 +0000 @@ -0,0 +1,39 @@ +Description: Fix spelling +Author: Andreas Tille +Last-Update: Mon, 25 Jan 2016 09:15:42 +0100 + +--- a/src/phylogeny/likeDist.cpp ++++ b/src/phylogeny/likeDist.cpp +@@ -145,10 +145,10 @@ MDOUBLE likeDist::giveDistanceThroughCTC + const sequence& s2, + const vector * weights, + MDOUBLE* score) const { +- // only in the case of homogenous model - work through pairwise EM like ++ // only in the case of homogeneous model - work through pairwise EM like + countTableComponentGam ctc; + if (_sp.categories() != 1) { +- errorMsg::reportError("this function only work for homogenous model."); ++ errorMsg::reportError("this function only work for homogeneous model."); + } + ctc.countTableComponentAllocatePlace(s1.getAlphabet()->size(),1); + for (int i=0; igetPijAccelerator();// note this is just a copy of the pointer. + stochasticProcess lsp(&lUni,lpijAcc); +@@ -997,7 +997,7 @@ Branch lengths optimization flag: + + -bn = no Branch lengths optimization + +- -bh = optimization using a homogenous model (no among-site-rate-variation) ++ -bh = optimization using a homogeneous model (no among-site-rate-variation) + + -bg = optimization using a Gamma model + diff -Nru rate4site-3.0.0/debian/rate4site.install rate4site-3.0.0/debian/rate4site.install --- rate4site-3.0.0/debian/rate4site.install 2013-10-04 15:02:16.000000000 +0000 +++ rate4site-3.0.0/debian/rate4site.install 1970-01-01 00:00:00.000000000 +0000 @@ -1,2 +0,0 @@ -usr/bin/rate4site -usr/share/man/* diff -Nru rate4site-3.0.0/debian/rules rate4site-3.0.0/debian/rules --- rate4site-3.0.0/debian/rules 2013-10-01 18:57:04.000000000 +0000 +++ rate4site-3.0.0/debian/rules 2016-01-25 08:14:22.000000000 +0000 @@ -1,18 +1,10 @@ #!/usr/bin/make -f #export DH_VERBOSE=1 -export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) -export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) -export CXXFLAGS:=$(shell dpkg-buildflags --get CXXFLAGS) -export LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) - -.PHONY: override_dh_strip -override_dh_strip: - dh_strip --dbg-package=rate4site-dbg +%: + dh $@ --parallel --with autotools_dev get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs -%: - dh $@ --parallel --with autotools_dev File /tmp/tmpaUOBoF/041CSdTpSj/rate4site-3.0.0/debian/upstream is a regular file while file /tmp/tmpaUOBoF/aB1ct2qrNs/rate4site-3.0.0/debian/upstream is a directory