debian/control

@@ -5,7 +5,9 @@ Uploaders: Andreas Tille <tille@debian.org>,
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 12~),
+               dh-exec,
                libglib2.0-dev,
+               time,
                valgrind
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/libarb

debian/copyright

@@ -210,140 +210,8 @@ License: ARB
  9. July 2008
  Ralf Westram <westram@arb-home.de>
 
-Files: GDE/*
-Copyright: 2004-2008 The Board of Trustees of the University of Illinois and by Steven Smith
-License: GDE
-  * The Genetic Data Environment (GDE) software and documentation are not in the
-    public domain. Portions of this code are owned and copyrighted by the
-    The Board of Trustees of the University of Illinois and by Steven Smith.
-    External functions used by GDE are the property of their authors.
-    This release of the GDE program and documentation may not be sold, or
-    incorporated into a commercial product, in whole or in part without the
-    expressed written consent of the University of Illinois and of its author,
-    Steven Smith.
-  * All interested parties may redistribute the GDE as long as all copies are
-    accompanied by this documentation, and all copyright notices remain intact.
-    Parties interested in redistribution must do so on a non-profit basis,
-    charging only for cost of media. Modifications to the GDE core editor
-    should be forwarded to the author Steven Smith. External programs used
-    by the GDE are copyrighted by, and are the property of their respective
-    authors unless otherwise stated.
-
-Files: GDE/PHYLIP/*
-Copyright: (c) Copyright 1986-1993 by Joseph Felsenstein and the University
-  of Washington.
-License: PHYLIP_non-free
-  Permission is granted to copy this document provided that
-  no fee is charged for it and that this copyright notice is not removed.
-Comment: Remark from the Debian package maintainer Andreas Tille
- Phylp is not used in the binary package because the Debian
- package is used which is in the non-free part of Debian.
- Remark: After heavy discussion with the author of Phylip it
- was not possible to convince him to use a free license.
-
-Files: GDE/SUPPORT/CAP2.c
-Copyright: (C) 1991   Xiaoqiu Huang
-License: CAP2_non-free
- The distribution of the program is granted provided no charge
- is made and the copyright notice is included.
-Comment: Remark from the Debian package maintainer Andreas Tille
- I was unable to find a source URL where this program which is
- claimed as external can be downloaded.
-
-Files: CONVERTALN/*
-Copyright: (C) 1992 Wen-Min Kuan
-License: ARP_permissive
- The files in this directory do not contain an explicite license
- statement.  It has to be assumed that the license is the same as the
- general usage and redistribution license for Arb and the authors of
- Arb got a permission to distribute this code in their product.
- .
- This paragraph was just added to the copyright file to mention that
- there is some copyrighted work which was not mentioned above.
-Comment: convert_aln --  an alignment(or sequence) converter written
- by Wen-Min Kuan for the Ribsomal Database Project(RDP), April 28, 1992.
- .
- Remark from the Debian package maintainer Andreas Tille:
- I was unable to find a source URL where this program which is
- claimed as external can be downloaded.
-
-Files: GDE/FASTDNAML/*
-Copyright: (C) 1998, 1999, 2000 by Gary J. Olsen,
- 1986 - 1990 by the University of Washington and Joseph Felsenstein.
-License: GPL
-Comment: Remark from the Debian package maintainer Andreas Tille:
- This is not used in the binary package because it is available as
- official Debian package and has a free license (see this package).
-
-Files: GDE/RAxML/a*
-Copyright: (C) 2004-2008 Alexandros Stamatakis, Michael Ott, Thomas Ludwig
-License: GPL
-Comment: There is also a file GDE/RAxML/softwaredisclaimer in this directory
- which contains some license text which might be provided in a private
- mail or whatever from the RAxML authors to the Arb authors.  The relevance
- of this file is completely unclear because RAxML as it can be obtained from
- http://icwww.epfl.ch/~stamatak/index-Dateien/Page443.htm is GPLed and the
- remaining files in this directory are neither copyrighted by the RAxML
- authors nor do they feature a similar license statement.  This file is
- subject for clarification by the Arb authors.
-
-Files: GDE/RAxML/c* GDE/RAxML/p*
-Copyright: (C) 1993-2002 by the University of Washington.
- Written by Joseph Felsenstein, Hisashi Horino, and others
-License: RAxML_non-free
- Permission is granted to copy and use this program provided no
- fee is charged for it and provided that this copyright notice is not
- removed.
-
-Files: GDE/RAxML/g*
-Copyright: (C) 1987, 1993, 1994
- The Regents of the University of California.  All rights reserved.
-License: BSD-3-clause
- Copyright (c) The Regents of the University of California.
- All rights reserved.
- .
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions
- are met:
- 1. Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimer.
- 2. Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimer in the
-    documentation and/or other materials provided with the distribution.
- 3. Neither the name of the University nor the names of its contributors
-    may be used to endorse or promote products derived from this software
-    without specific prior written permission.
- .
- THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED.  IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
- OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
- HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
- LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
- OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- SUCH DAMAGE.
-
-Files: GDE/TREEPUZZLE/*
-Copyright: (C) 1995-1999 Korbinian Strimmer and Arndt von Haeseler
- (C) 1999-2001 Heiko A. Schmidt, Korbinian Strimmer,Martin Vingron,
-           Arndt von Haeseler
-License: GPL
-Comment: This code is not used in the binary package because it is available
- as official Debian package and has a free license (see this package).
-
-Files: READSEQ/*
-Copyright: 1990-1993 D. Gilbert <gilbertd@bio.indiana.edu>
-License: PD
- readseq is public domain software
-Comment: This code is not used in the binary package because it is
- available as official Debian package and has a free license (see this
- package).
-
 Files: debian/*
-Copyright: (C) 2008-2013 Andreas Tille <tille@debian.org>
+Copyright: (C) 2008-2019 Andreas Tille <tille@debian.org>
 License: GPL
 
 License: GPL

debian/libarb-dev.install

-debian/tmp-dev/INCLUDE/*  usr/include/arb
-debian/tmp-dev/*_COM      usr/lib/arb
-debian/tmp-dev/SL         usr/lib/arb
-
+#!/usr/bin/dh-exec
+SL/*/*.a	usr/lib/${DEB_HOST_MULTIARCH}/arb

debian/libarb-dev.links

-usr/include/arb usr/lib/arb/INCLUDE
+# This is probably not needed any more - if at all it should probably be usr/lib/${DEB_HOST_MULTIARCH}/arb/INCLUDE
+# usr/include/arb usr/lib/arb/INCLUDE

debian/libarb.install

-debian/tmp/lib/*.so           usr/lib/arb/lib
+#!/usr/bin/dh-exec
+lib/*.so           usr/lib/${DEB_HOST_MULTIARCH}/arb

debian/patches/fix_main_makefile.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 05 Jun 2019 15:03:30 +0200
+Description: Strip everything from ARB Makefiles that's not contained in the
+ free library parts.
+
 --- a/Makefile
 +++ b/Makefile
+@@ -201,8 +201,8 @@ ifeq ($(DEBUG),0)
+ endif
+ 
+ ifeq ($(DEBIAN),1)
+-	lflags += -rpath=/usr/lib/arb/lib -z relro
+-	clflags += -Wl,-rpath=/usr/lib/arb/lib -Wl,-z,relro
++	lflags += -z relro
++	clflags += -Wl,-z,relro
+ endif
+ 
+ ifeq ($(DEBUG),1)
 @@ -705,7 +705,7 @@ ifeq ($(strip $(CONFIG_MAKEFILE_FOUND)),
  		@echo '$(ARBHOME)/$@:1: has been generated.'
  		@echo 'Please edit $@ to configure your system!'

debian/patches/fix_makefiles.patch

---- a/CORE/Makefile
-+++ b/CORE/Makefile
-@@ -12,6 +12,13 @@ GENERATED_HEADERS= \
- 	arb_diff.h \
- 	arb_match.h \
- 
-+ARBHOME=..
-+A_CXX=$(CXX)
-+shared_cflags= -fPIC -I../INCLUDE -I. -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include/ -DDEBUG
-+SHARED_LIB_SUFFIX=so
-+LINK_SHARED_LIB := $(A_CXX) $(clflags) -shared $(GCOVFLAGS) -o# link shared lib
-+MAIN=libCORE.a
-+
- LIB_SHARED=../lib/$(MAIN:.a=).$(SHARED_LIB_SUFFIX)
- 
- # MAIN contains .a (instead of wanted .so). Translate via do_...-target

debian/patches/ignore_unneeded_stuff.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Wed, 05 Jun 2019 15:03:30 +0200
+Description: Some scripts are referencing things that are not available in
+ the stripped down free library part.  Just patch this out.
+
 --- a/SOURCE_TOOLS/generate_all_links.sh
 +++ b/SOURCE_TOOLS/generate_all_links.sh
 @@ -1,7 +1,7 @@

debian/rules

@@ -7,6 +7,7 @@
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 include /usr/share/dpkg/default.mk
+libdevel=$(DEB_SOURCE)-dev
 
 ARBHOME=$(CURDIR)
 
@@ -63,6 +64,12 @@ override_dh_auto_clean: config.makefile
 	find -name \*.log -a ! -name phyml-manual.log -print0 | xargs -0 rm -f
 	rm -f TEMPLATES/arb_build.h
 
+override_dh_install:
+	dh_install
+	mkdir -p debian/$(libdevel)/usr/include/arb
+	install INCLUDE/*.h INCLUDE/*.hxx debian/$(libdevel)/usr/include/arb
+	rm -rf debian/$(libdevel)/usr/include/arb/valgrind.h
+
 override_dh_strip:
 	# Fix rpath issue (once libarb is installed)
 	if [ -e debian/libarb/usr/lib/arb/lib/ARB.so ] ; then \
@@ -73,10 +80,3 @@ override_dh_strip:
 
 override_dh_installchangelogs:
 	dh_installchangelogs arb_CHANGES.txt
-
-override_dh_shlibdeps:
-	dh_shlibdeps -a -l debian/libarb/usr/lib
-
-override_dh_fixperms:
-	dh_fixperms
-	chmod 0644 debian/libarb-dev/usr/include/arb/xml.hxx