debian/README.source

+The license was asked to be clarified in an email to Prof. D. Wilson on
+June 28th, 2018. He replied at the very same day that there was
+"never a license file distributed with omegaMap". He "would be happy
+for the approrpiate GNU license to be applied".  Done.
+
+ ---
+     Steffen Möller <moeller@debian.org> 
\ No newline at end of file

debian/changelog

 omegamap (0.5-1) unstable; urgency=medium
 
-  * Initial release (Closes: #nnnn)  <nnnn is the bug number of your ITP>
+  * Initial release (Closes: #902940).
 
  -- Steffen Moeller <moeller@debian.org>  Thu, 28 Jun 2018 20:11:26 +0200

debian/copyright

@@ -4,18 +4,16 @@ Source: http://www.danielwilson.me.uk/omegaMap.html
 
 Files: *
 Copyright: 2005 Danny Wilson <daniel.wilson@bdi.ox.ac.uk>
-License: <special license>
- <Put the license of the package here indented by 1 space>
- <This follows the format of Description: lines in control file>
- .
- <Including paragraphs>
+License: GPL-3
 
 Files: debian/*
 Copyright: 2018 Steffen Moeller <moeller@debian.org>
-License: GPL-2+
+License: GPL-3
+
+License: GPL-3
  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
+ the Free Software Foundation; either version 3 of the License, or
  (at your option) any later version.
  .
  This package is distributed in the hope that it will be useful,
@@ -27,4 +25,4 @@ License: GPL-2+
  along with this program. If not, see <https://www.gnu.org/licenses/>
  .
  On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".

debian/omegamap-doc.doc-base

+Document: omegamap
+Title: Debian omegaMap Manual
+Author: Daniel Wilson
+Abstract: This manual describes what omegaMap is
+ and how it can be used.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/omegamap/documentation.pdf
+

debian/omegamap-docs.docs

-README.Debian
-README.source

debian/omegamap.doc-base.EX

-Document: omegamap
-Title: Debian omegamap Manual
-Author: <insert document author here>
-Abstract: This manual describes what omegamap is
- and how it can be used to
- manage online manuals on Debian systems.
-Section: unknown
-
-Format: debiandoc-sgml
-Files: /usr/share/doc/omegamap/omegamap.sgml.gz
-
-Format: postscript
-Files: /usr/share/doc/omegamap/omegamap.ps.gz
-
-Format: text
-Files: /usr/share/doc/omegamap/omegamap.text.gz
-
-Format: HTML
-Index: /usr/share/doc/omegamap/html/index.html
-Files: /usr/share/doc/omegamap/html/*.html

debian/patches/Makefile.patch

@@ -6,7 +6,7 @@ Index: omegamap/makefile
  headers = omegaMap.h $(myutils)
  idir = "./"
  OLEVEL = 0
-+CXXFLAGS = -w -O2
++CXXFLAGS ?= -w -O2
  
  ## INSTRUCT MAKE TO MAKE MULTIPLE GOALS
 -.PHONY : all
@@ -22,23 +22,23 @@ Index: omegamap/makefile
  
  omegaMapTP : likelihood.TP.o $(objects)
 -	-g++ -w -O3 -o omegaMapTP likelihood.TP.o $(objects)
-+	-g++ $(CXXFLAGS) -o omegaMapTP likelihood.TP.o $(objects) $(LDFLAGS)
++	g++ $(CXXFLAGS) -o omegaMapTP likelihood.TP.o $(objects) $(LDFLAGS)
  
  summarize : summarize.o
 -	-g++ -w -O3 -o summarize summarize.o
-+	-g++ $(CXXFLAGS) -o summarize summarize.o $(LDFLAGS)
++	g++ $(CXXFLAGS) -o summarize summarize.o $(LDFLAGS)
  
  decode : decode.o likelihood.o omegaMap.o io.o mcmc.o tools.o
 -	-g++ -w -O3 -o decode decode.o likelihood.o omegaMap.o io.o mcmc.o tools.o
-+	-g++ $(CXXFLAGS) -o decode decode.o likelihood.o omegaMap.o io.o mcmc.o tools.o $(LDFLAGS)
++	g++ $(CXXFLAGS) -o decode decode.o likelihood.o omegaMap.o io.o mcmc.o tools.o $(LDFLAGS)
  
  order : order.o
 -	-g++ -w -O3 -o order order.o
-+	-g++ $(CXXFLAGS) -o order order.o $(LDFLAGS)
++	g++ $(CXXFLAGS) -o order order.o $(LDFLAGS)
  
  permute: permute.o
 -	-g++ -w -O3 -o permute permute.o
-+	-g++ $(CXXFLAGS) -o permute permute.o $(LDFLAGS)
++	g++ $(CXXFLAGS) -o permute permute.o $(LDFLAGS)
  
  ## COMPILE
  main.o : main.cpp $(headers)
@@ -59,34 +59,35 @@ Index: omegamap/makefile
  
  likelihood.TP.o : likelihood.cpp $(headers)
 -	-g++ -w -O3 -c -o likelihood.TP.o likelihood.cpp -I$(idir) -D_TESTPRIOR
-+	-g++ $(CXXFLAGS) -c -o likelihood.TP.o likelihood.cpp -I$(idir) -D_TESTPRIOR
++	g++ $(CXXFLAGS) -c -o likelihood.TP.o likelihood.cpp -I$(idir) -D_TESTPRIOR
  
  mcmc.o : mcmc.cpp $(headers)
  	g++ -w -O$(OLEVEL) -c -o mcmc.o mcmc.cpp -I$(idir)
  
  tools.o : tools.c paml.h
 -	gcc -w -O3 -c -o tools.o tools.c -I$(idir)
-+	gcc $(CXXFLAGS) -c -o tools.o tools.c -I$(idir)
++	gcc $(CFLAGS) -c -o tools.o tools.c -I$(idir)
  
  summarize.o : summarize.cpp $(headers)
 -	-g++ -w -O3 -c -o summarize.o summarize.cpp -I$(idir)
-+	-g++ $(CXXFLAGS) -c -o summarize.o summarize.cpp -I$(idir)
++	g++ $(CXXFLAGS) -c -o summarize.o summarize.cpp -I$(idir)
  
  decode.o : decode.cpp decode.h $(headers)
 -	-g++ -w -O3 -c -o decode.o decode.cpp -I$(idir)
-+	-g++ $(CXXFLAGS) -c -o decode.o decode.cpp -I$(idir)
++	g++ $(CXXFLAGS) -c -o decode.o decode.cpp -I$(idir)
  
  order.o : order.cpp myerror.h random.h vector.h utils.h
 -	-g++ -w -O3 -c -o order.o order.cpp -I$(idir)
-+	-g++ $(CXXFLAGS) -c -o order.o order.cpp -I$(idir)
++	g++ $(CXXFLAGS) -c -o order.o order.cpp -I$(idir)
  
  permute.o : permute.cpp $(myutils)
 -	-g++ -w -O3 -c -o permute.o permute.cpp -I$(idir)
-+	-g++ $(CXXFLAGS) -c -o permute.o permute.cpp -I$(idir)
++	g++ $(CXXFLAGS) -c -o permute.o permute.cpp -I$(idir)
  
  ## MAKE CLEAN
  clean :
- 	-rm $(objects) likelihood.o likelihood.TP.o summarize.o decode.o order.o permute.o
+-	-rm $(objects) likelihood.o likelihood.TP.o summarize.o decode.o order.o permute.o
++	rm -f $(objects) likelihood.o likelihood.TP.o summarize.o decode.o order.o permute.o
 +
 +distclean: clean
 +	rm -f $(binaries) *.o

debian/rules

@@ -7,3 +7,7 @@ export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
 
 %:
 	dh $@
+
+
+override_dh_compress:
+	dh_compress -X.pdf