[med-svn] [Git][med-team/libarb][master] 3 commits: Build some first packages in pbuilder
Andreas Tille
gitlab at salsa.debian.org
Fri Jun 7 09:33:08 BST 2019
Andreas Tille pushed to branch master at Debian Med / libarb
Commits:
8c48d38a by Andreas Tille at 2019-06-07T08:17:53Z
Build some first packages in pbuilder
- - - - -
fc02f124 by Andreas Tille at 2019-06-07T08:26:32Z
Fix some issues in packaging
- - - - -
634979f0 by Andreas Tille at 2019-06-07T08:30:47Z
More sensible location of the lib - if ARB might rely on a lib subdirectory this should be provide as symlink in the arb package
- - - - -
9 changed files:
- debian/control
- debian/copyright
- debian/libarb-dev.install
- debian/libarb-dev.links
- debian/libarb.install
- debian/patches/fix_main_makefile.patch
- − debian/patches/fix_makefiles.patch
- debian/patches/ignore_unneeded_stuff.patch
- debian/rules
Changes:
=====================================
debian/control
=====================================
@@ -5,7 +5,9 @@ Uploaders: Andreas Tille <tille at 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 at 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 at 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 at debian.org>
+Copyright: (C) 2008-2019 Andreas Tille <tille at debian.org>
License: GPL
License: GPL
=====================================
debian/libarb-dev.install
=====================================
@@ -1,4 +1,2 @@
-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/${DEB_HOST_MULTIARCH}/arb
=====================================
debian/libarb-dev.links
=====================================
@@ -1 +1,2 @@
-usr/include/arb usr/lib/arb/INCLUDE
+# This is probably not needed any more - if at all it should probably be usr/lib/${DEB_HOST_MULTIARCH}/arb/INCLUDE
+# usr/include/arb usr/lib/arb/INCLUDE
=====================================
debian/libarb.install
=====================================
@@ -1 +1,2 @@
-debian/tmp/lib/*.so usr/lib/arb/lib
+#!/usr/bin/dh-exec
+lib/*.so usr/lib/${DEB_HOST_MULTIARCH}/arb
=====================================
debian/patches/fix_main_makefile.patch
=====================================
@@ -1,5 +1,21 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 05 Jun 2019 15:03:30 +0200
+Description: Strip everything from ARB Makefiles that's not contained in the
+ free library parts.
+
--- a/Makefile
+++ b/Makefile
+@@ -201,8 +201,8 @@ ifeq ($(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 $@ to configure your system!'
=====================================
debian/patches/fix_makefiles.patch deleted
=====================================
@@ -1,16 +0,0 @@
---- a/CORE/Makefile
-+++ b/CORE/Makefile
-@@ -12,6 +12,13 @@ GENERATED_HEADERS= \
- arb_diff.h \
- arb_match.h \
-
-+ARBHOME=..
-+A_CXX=$(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=).$(SHARED_LIB_SUFFIX)
-
- # MAIN contains .a (instead of wanted .so). Translate via do_...-target
=====================================
debian/patches/ignore_unneeded_stuff.patch
=====================================
@@ -1,3 +1,8 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 05 Jun 2019 15:03:30 +0200
+Description: Some scripts are referencing things that are not available in
+ the stripped down free library part. Just patch this out.
+
--- a/SOURCE_TOOLS/generate_all_links.sh
+++ b/SOURCE_TOOLS/generate_all_links.sh
@@ -1,7 +1,7 @@
=====================================
debian/rules
=====================================
@@ -7,6 +7,7 @@
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
include /usr/share/dpkg/default.mk
+libdevel=$(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
View it on GitLab: https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba
--
View it on GitLab: https://salsa.debian.org/med-team/libarb/compare/750c0303770c75c853296310866457d19c5b840f...634979f027dbb211c8496e339592cc412f9e8bba
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190607/7d1a429a/attachment-0001.html>
More information about the debian-med-commit
mailing list