[med-svn] r15223 - in trunk/packages/amap-align/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 22:10:51 UTC 2013
Author: tille
Date: 2013-11-20 22:10:51 +0000 (Wed, 20 Nov 2013)
New Revision: 15223
Added:
trunk/packages/amap-align/trunk/debian/install
trunk/packages/amap-align/trunk/debian/manpages
trunk/packages/amap-align/trunk/debian/patches/hardening.patch
Removed:
trunk/packages/amap-align/trunk/debian/amap.1.xml
trunk/packages/amap-align/trunk/debian/wrapper/
Modified:
trunk/packages/amap-align/trunk/debian/NEWS
trunk/packages/amap-align/trunk/debian/amap.1
trunk/packages/amap-align/trunk/debian/changelog
trunk/packages/amap-align/trunk/debian/compat
trunk/packages/amap-align/trunk/debian/control
trunk/packages/amap-align/trunk/debian/copyright
trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.6.diff
trunk/packages/amap-align/trunk/debian/patches/series
trunk/packages/amap-align/trunk/debian/rules
Log:
Mass changes for 2.2-4
Modified: trunk/packages/amap-align/trunk/debian/NEWS
===================================================================
--- trunk/packages/amap-align/trunk/debian/NEWS 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/NEWS 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1,11 +1,11 @@
amap-align (2.0-2) unstable; urgency=low
- * Previous versions of the package amap-align were shipping the program
- under a binary name (amap-align) which differed from the original one
- (amap) because there was already an amap program in Debian. Since this
- program has been removed from the Etch distribution, amap-align now
- provides its function through the program /usr/bin/align. To help the
- transition, a symbolic link, /usr/bin/amap-align, is provided, but may
- be supressed in the releases following Etch.
+ Previous versions of the package amap-align were shipping the program
+ under a binary name (amap-align) which differed from the original one
+ (amap) because there was already an amap program in Debian. Since this
+ program has been removed from the Etch distribution, amap-align now
+ provides its function through the program /usr/bin/align. To help the
+ transition, a symbolic link, /usr/bin/amap-align, is provided, but may
+ be supressed in the releases following Etch.
-- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 10 Mar 2007 12:59:02 +0900
Modified: trunk/packages/amap-align/trunk/debian/amap.1
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap.1 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/amap.1 2013-11-20 22:10:51 UTC (rev 15223)
@@ -17,7 +17,7 @@
\fBamap\fR [\fB\fIOPTION\fR\fR] [\fIMFAFILE\fR] [\fIMFAFILE\fR]
.SH "DESCRIPTION"
.PP
-AMAP is a tool to perform multiple alignment of peptidic sequences\. It utilizes posterior decoding, and a sequence\-annealing alignment, instead of the traditional progressive alignment method\. It is the only alignment program that allows to control the sensitivity / specificity tradeoff\. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation\.
+AMAP is a tool to perform multiple alignment of peptidic sequences\. It utilizes posterior decoding, and a sequence\-annealing alignment, instead of the traditional progressive alignment method\. It is the only alignment program that allows one to control the sensitivity / specificity tradeoff\. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation\.
.PP
In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score \- a new alignment accuracy measure, based on a metric for the multiple\-alignment space, which integrates sensitivity and specificity into a single balanced measure\. AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences\.
.PP
Deleted: trunk/packages/amap-align/trunk/debian/amap.1.xml
===================================================================
--- trunk/packages/amap-align/trunk/debian/amap.1.xml 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/amap.1.xml 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1,322 +0,0 @@
-<?xml version='1.0' encoding='ISO-8859-1'?>
-<?xml-stylesheet type="text/xsl"
- href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
-"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
-
- <!ENTITY dhfirstname "Charles">
- <!ENTITY dhsurname "Plessy>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "charles-debian-nospam at plessy.org">
- <!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhucpackage "<refentrytitle>AMAP</refentrytitle>">
- <!ENTITY dhpackage "amap">
- <!ENTITY dhrelease "2.2">
- <!ENTITY debian "<productname>Debian</productname>">
- <!ENTITY gnu "<acronym>GNU</acronym>">
- <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
- <!ENTITY dhtitle "User Manual">
-]>
-
-<!-- This manpage is inspired from the template of docbook-xsl 1.71.0.dfsg.1-1.1 -->
-
-<refentry>
- <refentryinfo>
- <title>&dhtitle;</title>
- <productname>&dhpackage;</productname>
- <releaseinfo role="version">&dhrelease;</releaseinfo>
- <authorgroup>
- <author>
- <firstname>Ariel</firstname>
- <surname>Schwartz</surname>
- <contrib>Upstream author of AMAP</contrib>
- <address>
- <email>sariel at cs.berkeley.edu</email>
- </address>
- </author>
- <author>
- <firstname>Chuong</firstname>
- <surname>Do</surname>
- <contrib>Wrote Probcons, on which AMAP is based.</contrib>
- </author>
- <author>
- <firstname>&dhfirstname;</firstname>
- <surname>&dhsurname;</surname>
- <contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib>
- <address>
- <email>&dhemail;</email>
- </address>
- </author>
- </authorgroup>
- <legalnotice>
- <para>
- AMAP, PROBCONS, and this manual page have been made freely available as PUBLIC DOMAIN software and hence are not subject to copyright in the United States. This system and/or any portion of the source code may be used, modified, or redistributed without restrictions. AMAP, PROBCONS and this manual page are distributed WITHOUT WARRANTY, express or implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss due to reliance on the program.
- </para>
- </legalnotice>
- </refentryinfo>
- <refmeta>
- &dhucpackage;
-
- &dhsection;
- </refmeta>
- <refnamediv>
- <refname>amap</refname>
-
- <refpurpose>Protein multiple alignment by sequence annealing</refpurpose>
- </refnamediv>
- <refsynopsisdiv>
- <cmdsynopsis>
- <command>amap</command>
-
- <arg choice="opt"><option><replaceable>OPTION</replaceable></option></arg>
-
- <arg><replaceable>MFAFILE</replaceable></arg>
- <arg choice="opt"><replaceable>MFAFILE</replaceable></arg>
- </cmdsynopsis>
- </refsynopsisdiv>
- <refsect1>
- <title>DESCRIPTION</title>
-
- <para>AMAP is a tool to perform multiple alignment of peptidic sequences. It utilizes posterior decoding, and a sequence-annealing alignment, instead of the traditional progressive alignment method. It is the only alignment program that allows to control the sensitivity / specificity tradeoff. It is based on the ProbCons source code, but uses alignment metric accuracy and eliminates the consistency transformation.</para>
-
- <para>In its default configuration, AMAP is tuned to maximize the expected Alignment Metric Accuracy (AMA) score - a new alignment accuracy measure, based on a metric for the multiple-alignment space, which integrates sensitivity and specificity into a single balanced measure. AMA is defined as the fraction of correctly aligned residues (either to another residue or to a gap) out of the total number of residues in all the sequences.</para>
-
- <para><command>&dhpackage;</command> aligns sequences provided in MFA format. This format consists of multiple sequences. Each sequence in MFA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (<quote>></quote>) symbol in the first column.</para>
-
- </refsect1>
- <refsect1>
- <title>OPTIONS</title>
-
- <variablelist>
- <varlistentry>
- <term><option>-clustalw</option>
- </term>
- <listitem>
- <para>use CLUSTALW output format instead of MFA</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-c</option>
- <option>--consistency</option> <varname>REPS</varname>
- </term>
- <listitem>
- <para>use 0 <= <varname>REPS</varname> <= 5 (default: 0) passes of consistency transformation</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-ir</option>
- <option>--iterative-refinement</option> <varname>REPS</varname>
- </term>
- <listitem>
- <para>use 0 <= <varname>REPS</varname> <=1000 (default: 0) passes of iterative-refinement</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-pre</option>
- <option>--pre-training</option> <varname>REPS</varname>
- </term>
- <listitem>
- <para>use 0 <= <varname>REPS</varname> <= 20 (default: 0) rounds of pretraining</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-pairs</option>
- </term>
- <listitem>
- <para>generate all-pairs pairwise alignments</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-viterbi</option>
- </term>
- <listitem>
- <para>use Viterbi algorithm to generate all pairs (automatically enables <option>-pairs</option>)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-v</option>
- <option>--verbose</option>
- </term>
- <listitem>
- <para>Report progress while aligning (default: off)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-annot</option> <filename>FILENAME</filename> </term>
- <listitem>
- <para>write annotation for multiple alignment to <filename>FILENAME</filename></para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-t</option>
- <option>--train</option> <filename>FILENAME</filename>
- </term>
- <listitem>
- <para>compute EM transition probabilities, store in <filename>FILENAME</filename> (default: no training)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-e</option>
- <option>--emissions</option>
- </term>
- <listitem>
- <para>also reestimate emission probabilities (default: off)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-p</option>
- <option>--paramfile</option> <filename>FILENAME</filename>
- </term>
- <listitem>
- <para>read parameters from <filename>FILENAME</filename> (default: )</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-a</option>
- <option>--alignment-order</option>
- </term>
- <listitem>
- <para>print sequences in alignment order rather than input order (default: off)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-g</option>
- <option>--gap-factor</option>
- <varname>GF</varname>
- </term>
- <listitem>
- <para>use <varname>GF</varname> as the gap-factor parameter, set to 0 for best sensitivity, higher values for better specificity (default: 0.5)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-w</option>
- <option>--edge-weight-threshold</option>
- <varname>W</varname>
- </term>
- <listitem>
- <para>stop the sequence annealing process when best edge has lower weight than <varname>W</varname>, set to 0 for best sensitivity, higher values for better specificity (default: 0)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-prog</option>
- <option>--progressive</option>
- </term>
- <listitem>
- <para>use progressive alignment instead of sequence annealing alignment (default: off)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-noreorder</option>
- <option>--no-edge-reordering</option>
- </term>
- <listitem>
- <para>disable reordering of edges during sequence annealing alignment (default: off)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-maxstep</option>
- <option>--use-max-stepsize</option>
- </term>
- <listitem>
- <para>use maximum improvement step size instead of tGf edge ranking (default: off)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term><option>-print</option>
- <option>--print-posteriors</option>
- </term>
- <listitem>
- <para>only print the posterior probability matrices (default: off)</para>
- </listitem>
- </varlistentry>
-
- <varlistentry>
- <term>
- <option>-gui</option>
- <varname>START</varname>
- <varname>STEP</varname>
- </term>
- <listitem>
- <para> print output for the AMAP Display Java based GUI (default: ) starting at weight <varname>START</varname> (default: infinity) with step size <varname>STEP</varname> (default: )</para>
- </listitem>
- </varlistentry>
- </variablelist>
- </refsect1>
-
- <refsect1>
- <title>
- EXAMPLES
- </title>
- <para>
- To run AMAP with the default options change to the <filename>align</filename> directory and type:
- </para>
- <para>
- <command>% amap <multi-fasta-file-name></command>
- </para>
- <para>
- If no file name is provided the list of options are printed.
- </para>
- <para>
- In order to use the AMAP Display run AMAP with the -gui option, and save the output to a file, then use the file as the input to AmapDisplay. For example, type:
- </para>
- <para>
- <command>% align/amap -gui examples/BB12020.tfa > examples/BB12020.tfa.out</command>
- </para>
- <para>
- <command>% java -jar display/AmapDisplay.jar examples/BB12020.tfa.out</command>
- </para>
- <para>
- (on Debian systems, the <filename>examples</filename> directory is in <filename>/usr/share/doc/amap-align/examples</filename>
- </para>
- </refsect1>
-
- <refsect1>
- <title>
- NOTE
- </title>
-
- <para>In older versions ( < 2.0-1) of the package for &debian; systems, the <command>amap</command> command was renamed <command>amap-align</command> because there was already another tool called <command>amap</command> (which performs some computer network diagnostics). A symbolic link <command>amap-align</command> is still provided for upgrade purposes but will be removed in Debian releases posterior to Etch (Debian 4.0).</para>
- </refsect1>
-
- <refsect1>
- <title>SEE ALSO</title>
- <para>
- The current version of AMAP uses the PROBCONS 1.09 code base for some of the input/output procedures, and for the calculation of posterior probabilities (see PROBCONS.README in <filename>/usr/share/doc/amap-align/</filename>). Future releases might implement the algorithm using a new independent code base.
- </para>
-
- <para>
- On &debian; systems, <citerefentry><refentrytitle>probcons</refentrytitle><manvolnum>1</manvolnum></citerefentry> is available in the probcons package.</para>
- </refsect1>
-
- <refsect1>
- <title>REFERENCES</title>
- <para>
- For more details on AMAP and AMA, see Schwartz, Ariel S., Myers, Eugene W., and Pachter, Lior. Alignment Metric Accuracy (Submitted for publication). For more details on sequence-annealing, see Schwartz, Ariel S. and Pachter, Lior. Multiple Alignment by Sequence Annealing (Submitted for publication).
- </para>
-
- <para>
- PROBCONS was published in Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.
- </para>
- </refsect1>
-
-</refentry>
Modified: trunk/packages/amap-align/trunk/debian/changelog
===================================================================
--- trunk/packages/amap-align/trunk/debian/changelog 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/changelog 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1,14 +1,17 @@
-amap-align (2.2-5) UNRELEASED; urgency=low
+amap-align (2.2-4) unstable; urgency=low
* debian/README.Debian: Mentioning that latest source is not available
online any more
* debian/source/format: 3.0 (quilt)
* debian/upstream: Add citation information
* debian/control:
- - Standards-Version: 3.9.3 (no changes needed)
- - Fixed Vcs fields
+ - cme fix dpkg-control
+ - canonical Vcs fields
+ - debhelper 9
+ * remove unneeded amap-align wrapper as announced previously (NEWS)
+ * debian/patches/hardening.patch: Propagate hardening options
- -- Andreas Tille <tille at debian.org> Wed, 25 Apr 2012 08:09:52 +0200
+ -- Andreas Tille <tille at debian.org> Thu, 14 Nov 2013 13:46:11 +0100
amap-align (2.2-3) unstable; urgency=low
Modified: trunk/packages/amap-align/trunk/debian/compat
===================================================================
--- trunk/packages/amap-align/trunk/debian/compat 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/compat 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/amap-align/trunk/debian/control
===================================================================
--- trunk/packages/amap-align/trunk/debian/control 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/control 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1,20 +1,19 @@
Source: amap-align
-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>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), quilt
-Standards-Version: 3.9.3
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/amap-align/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/amap-align/trunk/
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/amap-align/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/amap-align/trunk/
X-Homepage: http://bio.math.berkeley.edu/amap/ - upstream seems to be dead
Package: amap-align
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Conflicts: amap (<= 4.8-1)
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
Description: Protein multiple alignment by sequence annealing
AMAP is a command line tool to perform multiple alignment of peptidic
sequences. It utilizes posterior decoding, and a sequence-annealing
Modified: trunk/packages/amap-align/trunk/debian/copyright
===================================================================
--- trunk/packages/amap-align/trunk/debian/copyright 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/copyright 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1,15 +1,8 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Charles Plessy <charles-debian-nospam at plessy.org>
-X-Debinized-Date: Sun, 9 Jul 2006 12:53:25 +0900.
-X-Source-Downloaded-From: http://bio.math.berkeley.edu/amap/download
-X-Note: This download area as well as the homepage vanished
-X-Upstream-Author: 2005—2007 Ariel Schwartz <sariel at cs.berkeley.edu>
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Author: Ariel Schwartz <sariel at cs.berkeley.edu>
+Source: http://bio.math.berkeley.edu/amap/download
+ This download area as well as the homepage vanished
-Files: debian/*
-Copyright: © 2007 David Paleino <d.paleino at gmail.com>
- © 2006—2008 Charles Plessy <chalres-debian-nospam at plessy.org>
-License: Same as AMAP itelf
-
Files: display/*
Copyright: © 2007 Michael E. Smoot
License: GPL-2+
@@ -26,11 +19,15 @@
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-X-Comment: On Debian systems, the complete text of the GNU General Public
+ .
+ On Debian systems, the complete text of the GNU General Public
License can be found in `/usr/share/common-licenses/GPL'.
Files: *
+Copyright: 2005—2007 Ariel Schwartz <sariel at cs.berkeley.edu>
License: PD
+
+License: PD
The current version of AMAP uses the PROBCONS 1.09 code base for some of the
input/output procedures, and for the calculation of posterior probabilities
(see PROBCONS.README).
@@ -50,3 +47,9 @@
without restrictions. PROBCONS is distributed WITHOUT WARRANTY, express or
implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for loss
due to reliance on the program.
+
+Files: debian/*
+Copyright: © 2007 David Paleino <d.paleino at gmail.com>
+ © 2006—2008 Charles Plessy <chalres-debian-nospam at plessy.org>
+ © 2011-2013 Andreas Tille <tille at debian.org>
+License: PD
Added: trunk/packages/amap-align/trunk/debian/install
===================================================================
--- trunk/packages/amap-align/trunk/debian/install (rev 0)
+++ trunk/packages/amap-align/trunk/debian/install 2013-11-20 22:10:51 UTC (rev 15223)
@@ -0,0 +1 @@
+align/amap usr/bin
Added: trunk/packages/amap-align/trunk/debian/manpages
===================================================================
--- trunk/packages/amap-align/trunk/debian/manpages (rev 0)
+++ trunk/packages/amap-align/trunk/debian/manpages 2013-11-20 22:10:51 UTC (rev 15223)
@@ -0,0 +1 @@
+debian/*.1
Modified: trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.6.diff
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.6.diff 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/patches/fix-gcc-4.6.diff 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1,3 +1,7 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Mon, 02 May 2011 16:30:17 +0200
+Description: Add header file needed for gcc-4.6
+
--- amap-align-2.2.orig/align/SafeVector.h
+++ amap-align-2.2/align/SafeVector.h
@@ -10,6 +10,7 @@
Added: trunk/packages/amap-align/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/hardening.patch (rev 0)
+++ trunk/packages/amap-align/trunk/debian/patches/hardening.patch 2013-11-20 22:10:51 UTC (rev 15223)
@@ -0,0 +1,24 @@
+Authoe: Andreas Tille <tille at debian.org>
+LastChanged: Thu, 14 Nov 2013 13:46:11 +0100
+Description: Propagate hardening options
+
+--- a/align/Makefile
++++ b/align/Makefile
+@@ -26,7 +26,7 @@ OTHERFLAGS = -DNumInsertStates=1 -DVERSI
+
+ # release mode
+ #CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -mmmx -msse -msse2 -mfpmath=sse -march=pentium4 -mcpu=pentium4 -funroll-loops -fomit-frame-pointer
+-CXXFLAGS = -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
++CXXFLAGS += -O3 -W -Wall -pedantic -DNDEBUG $(OTHERFLAGS) -funroll-loops
+
+ ################################################################################
+ # 3) Dependencies
+@@ -38,7 +38,7 @@ TARGETS = amap
+ all : $(TARGETS)
+
+ amap : MultiSequenceDag.h MultiSequence.h ProbabilisticModel.h ScoreType.h Sequence.h FileBuffer.h SparseMatrix.h EvolutionaryTree.h Defaults.h SafeVector.h Amap.cc
+- $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc
++ $(CXX) $(CXXFLAGS) -lm -o amap Amap.cc $(LDFLAGS)
+
+ .PHONY : clean
+ clean:
Modified: trunk/packages/amap-align/trunk/debian/patches/series
===================================================================
--- trunk/packages/amap-align/trunk/debian/patches/series 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/patches/series 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1,2 +1,3 @@
fix-gcc-4.3.diff
fix-gcc-4.6.diff
+hardening.patch
Modified: trunk/packages/amap-align/trunk/debian/rules
===================================================================
--- trunk/packages/amap-align/trunk/debian/rules 2013-11-20 22:09:20 UTC (rev 15222)
+++ trunk/packages/amap-align/trunk/debian/rules 2013-11-20 22:10:51 UTC (rev 15223)
@@ -1,14 +1,6 @@
#!/usr/bin/make -f
# -*- makefile -*-
-# Build rules for the Debian package probcons
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
-# Modifications by Charles Plessy during the years 2006-8 can also
-# be used without restriction.
-
XP=xsltproc \
-''-nonet \
-''-param man.charmap.use.subset "0" \
@@ -16,59 +8,12 @@
-''-param make.single.year.ranges "1" \
-o debian/
-pkg=amap-align
+pkg := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+SRCDIR=align
-CFLAGS = -Wall -g
+%:
+ dh $@ --sourcedirectory=$(SRCDIR) --parallel
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-
-include /usr/share/quilt/quilt.make
-
-build: build-stamp
-build-stamp: patch
- dh_testdir
- $(MAKE) -C align
- touch $@
-
-amap.1: debian/amap.1.xml
- $(XP) $<
-
-clean: unpatch
- dh_testdir
- dh_testroot
- rm -f build-stamp
- [ ! -f align/Makefile ] || $(MAKE) -C align clean
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_prep
- dh_installdirs
-
-binary-indep: build install
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs
+override_dh_installexamples:
dh_installexamples
chmod 644 debian/$(pkg)/usr/share/doc/$(pkg)/examples/BB12020.tfa
- dh_install align/amap debian/wrapper/amap-align usr/bin/
- dh_installman debian/amap.1
- dh_link usr/share/man/man1/amap.1 usr/share/man/man1/amap-align.1
- dh_strip
- dh_compress
- dh_fixperms
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
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