debian/README.Debian

+lagan for Debian
+================
+
+There is a name space conflict with EMBOSS (see bug #914687).  This is
+specifically unfortunate since both packages are from the field of
+bioinformatics and it should be avoided.  (Remark: I even think that the
+choice of /usr/bin/chaos is a bit unfortunate in general since it is
+quite a generic name.)
+
+In Debian the package that has occupied a name first usually wins and
+the other package has to rename.  In this case I also think that EMBOSS
+is quite famous and has lots of users (according to Debian popularity
+contest which is measuring the number of users of a package).  Thus we
+need to choose a different name for chaos provided by lagan.
+
+For the moment this is solved by moving /usr/bin/chaos to
+/usr/lib/lagan/bin/chaos and provide a symlink /usr/bin/lagan_chaos.
+

debian/changelog

+lagan (2.0-3) unstable; urgency=medium
+
+  * Upload to unstable
+  * debhelper 11
+  * Drop useless get-orig-source target
+  * Remove trailing whitespace in debian/changelog
+  * Move /usr/bin/chaos to /usr/lib/lagan/bin
+    Closes: #914687
+  * debian/README.Debian: Document move of /usr/bin/chaos
+  * Propagate hardening and debug options
+
+ -- Andreas Tille <tille@debian.org>  Tue, 04 Dec 2018 08:36:52 +0100
+
 lagan (2.0-2) experimental; urgency=low
 
   * Initial release to experimental to invite peer review (Closes: #908215).

debian/compat

-10
+11

debian/control

 Source: lagan
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille@debian.org>, Steffen Moeller <moeller@debian.org>
+Uploaders: Andreas Tille <tille@debian.org>,
+           Steffen Moeller <moeller@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                libboost-dev
 Standards-Version: 4.2.1
 Vcs-Browser: https://salsa.debian.org/med-team/lagan

debian/lagan.install

 anchors		usr/bin
-chaos		usr/bin
+chaos		usr/lib/lagan/bin
 glocal		usr/bin
 mlagan		usr/bin
 prolagan	usr/bin

debian/lagan.links

+usr/lib/lagan/bin/chaos	usr/bin/lagan_chaos

debian/lagan.lintian-overrides

@@ -9,7 +9,7 @@ lagan: script-with-language-extension usr/bin/supermap.pl
 lagan: script-with-language-extension usr/bin/xmfa2mfa.pl
 lagan: binary-without-manpage usr/bin/anal_gloc.pl
 lagan: binary-without-manpage usr/bin/anchors
-lagan: binary-without-manpage usr/bin/chaos
+lagan: binary-without-manpage usr/bin/lagan_chaos
 lagan: binary-without-manpage usr/bin/glocal
 lagan: binary-without-manpage usr/bin/lagan.pl
 lagan: binary-without-manpage usr/bin/order

debian/patches/addTest.patch

+Author: Steffen Moeller
+Last-Update: 2018-09-07 15:08:19 +0200
+Description: Add primitive build time test
+
 Index: lagan/Makefile
 ===================================================================
 --- lagan.orig/Makefile

debian/patches/adjustPerlPaths.patch

+Author: Steffen Moeller
+Last-Update: 2018-09-07 15:08:19 +0200
+Description: Adjust Perl path
+
 Index: lagan/anal_gloc.pl
 ===================================================================
 --- lagan.orig/anal_gloc.pl

debian/patches/ambiuousEnd.patch

+Author: Steffen Moeller
+Last-Update: 2018-09-07 15:08:19 +0200
+Description: Fix build issue
+
 Index: lagan/src/glocal/rightinfluence.cpp
 ===================================================================
 --- lagan.orig/src/glocal/rightinfluence.cpp

debian/patches/hardening.patch

+Description: Propagate hardening options
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Tue, 04 Dec 2018 08:36:52 +0100
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,6 +1,6 @@
+ CC = gcc $(CFLAGS)
+ CPP = g++ $(CFLAGS)
+-CFLAGS = -O3 # -Wall -W
++CFLAGS += -O3 # -Wall -W
+ TRGT_DIR = ..
+ 
+ all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
+@@ -9,46 +9,46 @@ clean:
+ 	rm -f *.o *~ utils/*~ mlagan.purify core
+ 	(cd glocal; $(MAKE) clean)
+ ../anchors: anchors.c skiplist.c
+-	$(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
++	$(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c $(LDFLAGS)
+ ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
++	$(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG $(LDFLAGS)
+ ../order: order.c diagmatrix.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
++	$(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c $(LDFLAGS)
+ ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++	$(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG $(LDFLAGS)
+ ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+-	$(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++	$(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG $(LDFLAGS)
+ ../utils/bin2mf: utils/bin2mf.c
+-	$(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
++	$(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c $(LDFLAGS)
+ ../utils/bin2bl: utils/bin2bl.c
+-	$(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
++	$(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c $(LDFLAGS)
+ ../utils/cextract: utils/cextract.c
+-	$(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
++	$(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c $(LDFLAGS)
+ ../utils/cstat: utils/cstat.c
+-	$(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
++	$(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c $(LDFLAGS)
+ ../utils/contigorder: utils/contigorder.c
+-	$(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
++	$(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c $(LDFLAGS)
+ ../utils/getbounds: utils/getbounds.c
+-	$(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
++	$(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c $(LDFLAGS)
+ ../utils/getcontigpos: utils/getcontigpos.c
+-	$(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
++	$(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c $(LDFLAGS)
+ ../utils/getlength: utils/getlength.c
+-	$(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
++	$(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c $(LDFLAGS)
+ ../utils/getoverlap: utils/getoverlap.c
+-	$(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
++	$(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c $(LDFLAGS)
+ ../utils/rc: utils/rc.c
+-	$(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
++	$(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c $(LDFLAGS)
+ ../utils/seqmerge: utils/seqmerge.c
+-	$(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
++	$(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c $(LDFLAGS)
+ ../utils/scorealign: utils/scorealign.c
+-	$(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
++	$(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm $(LDFLAGS)
+ ../utils/scorecontigs: utils/scorecontigs.c
+-	$(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
++	$(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm $(LDFLAGS)
+ ../utils/fa2xfa: utils/fa2xfa.c
+-	$(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
++	$(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c $(LDFLAGS)
+ ../utils/overlay: utils/overlay.c
+-	$(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
++	$(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c $(LDFLAGS)
+ ../utils/Glue: utils/Glue.cpp
+-	$(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
++	$(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp $(LDFLAGS)
+ ../utils/dotplot: utils/dotplot.cpp
+-	$(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
++	$(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp $(LDFLAGS)

debian/patches/series

@@ -3,3 +3,4 @@ gcc-4.8.patch
 ambiuousEnd.patch
 addTest.patch
 adjustPerlPaths.patch
+hardening.patch

debian/rules

@@ -5,9 +5,8 @@
 %:
 	dh $@
 
-get-orig-source:
-	mkdir -p ../tarballs
-	uscan --verbose --force-download --repack-compression xz --destdir=../tarballs
+override_dh_auto_build:
+	dh_auto_build --sourcedirectory=src
 
 override_dh_auto_clean:
 	dh_auto_clean