[med-svn] [libgkarrays] 02/02: Inject as somewhat hackish packaging which avoids an extra libprogressbar package

Andreas Tille tille at debian.org
Mon Sep 12 11:02:19 UTC 2016


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository libgkarrays.

commit ac7a0a72f6fd184a01739ab2a1916428b4fc51f3
Author: Andreas Tille <tille at debian.org>
Date:   Mon Sep 12 13:01:00 2016 +0200

    Inject as somewhat hackish packaging which avoids an extra libprogressbar package
---
 debian/changelog                   |   5 +
 debian/compat                      |   1 +
 debian/control                     |  51 ++++
 debian/copyright                   | 536 +++++++++++++++++++++++++++++++++++++
 debian/patches/proper_soname.patch |  27 ++
 debian/patches/series              |   1 +
 debian/rules                       |  33 +++
 debian/source/format               |   1 +
 debian/upstream/metadata           |  10 +
 debian/watch                       |   3 +
 10 files changed, 668 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..468c308
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+libgkarrays (2.1.0-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #<bug>)
+
+ -- Andreas Tille <tille at debian.org>  Sat, 10 Sep 2016 23:41:37 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..f83e09a
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,51 @@
+Source: libgkarrays
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Anthony Boureux <Anthony.Boureux at gmail.com>,
+           Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               dh-autoreconf,
+               d-shlibs,
+               zlib1g-dev
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libgkarrays.git
+Vcs-Git: https://anonscm.debian.org/git/debian-med/libgkarrays.git
+Homepage: http://crac.gforge.inria.fr/gkarrays/
+
+Package: libgkarrays1
+Architecture: any
+Section: libs
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: library to query large collection of NGS sequences
+ Gk-arrays are provided as a simple-to-use C++ library dedicated to
+ queries on large collection of sequences as produced by high-throughput
+ sequencers (e.g. HiSeq 2000 from Illumina, 454 from Roche).
+ .
+ Gk-arrays index k-mers of reads and allow to answer different queries on
+ that read collection (e.g. how many reads share this k-mer? where does
+ this k-mer occur in the read collection?).
+ .
+ Gk-arrays consist of a space-efficient alternative to hash tables while
+ being similar in terms of query times.
+
+Package: libgkarrays-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         libgkarrays1 (= ${binary:Version})
+Description: library to query large collection of NGS sequences (development)
+ Gk-arrays are provided as a simple-to-use C++ library dedicated to
+ queries on large collection of sequences as produced by high-throughput
+ sequencers (e.g. HiSeq 2000 from Illumina, 454 from Roche).
+ .
+ Gk-arrays index k-mers of reads and allow to answer different queries on
+ that read collection (e.g. how many reads share this k-mer? where does
+ this k-mer occur in the read collection?).
+ .
+ Gk-arrays consist of a space-efficient alternative to hash tables while
+ being similar in terms of query times.
+ .
+ This is the development library for libgkarrays.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..8022221
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,536 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Gk-arrays
+Source: http://crac.gforge.inria.fr
+
+Files: *
+Copyright: © 2012-2014 by Nicolas PHILIPPE <nicolas.philippe at lirmm.fr>
+           © 2012-2014 by Mikaël SALSON    <mikael.salson at lifl.fr>
+           © 2012-2014 by Alban MANCHERON  <alban.mancheron at lirmm.fr>
+           © 2013-2014 by Jérôme Audoux <Jerome.Audoux at gmail.com>
+License: CeCILL
+
+Files: debian/*
+Copyright: 2014 Anthony Boureux <Anthony.Boureux at gmail.com>
+License: GPL-2+
+ 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
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://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".
+
+License: CeCILL
+ CeCILL FREE SOFTWARE LICENSE AGREEMENT
+ .
+     Notice
+ .
+ This Agreement is a Free Software license agreement that is the result
+ of discussions between its authors in order to ensure compliance with
+ the two main principles guiding its drafting:
+ .
+     * firstly, compliance with the principles governing the distribution
+       of Free Software: access to source code, broad rights granted to
+       users,
+     * secondly, the election of a governing law, French law, with which
+       it is conformant, both as regards the law of torts and
+       intellectual property law, and the protection that it offers to
+       both authors and holders of the economic rights over software.
+ .
+ The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
+ license are:
+ .
+ Commissariat  l'Energie Atomique - CEA, a public scientific, technical
+ and industrial research establishment, having its principal place of
+ business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
+ .
+ Centre National de la Recherche Scientifique - CNRS, a public scientific
+ and technological establishment, having its principal place of business
+ at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
+ .
+ Institut National de Recherche en Informatique et en Automatique -
+ INRIA, a public scientific and technological establishment, having its
+ principal place of business at Domaine de Voluceau, Rocquencourt, BP
+ 105, 78153 Le Chesnay cedex, France.
+ .
+ .
+     Preamble
+ .
+ The purpose of this Free Software license agreement is to grant users
+ the right to modify and redistribute the software governed by this
+ license within the framework of an open source distribution model.
+ .
+ The exercising of these rights is conditional upon certain obligations
+ for users so as to preserve this status for all subsequent redistributions.
+ .
+ In consideration of access to the source code and the rights to copy,
+ modify and redistribute granted by the license, users are provided only
+ with a limited warranty and the software's author, the holder of the
+ economic rights, and the successive licensors only have limited liability.
+ .
+ In this respect, the risks associated with loading, using, modifying
+ and/or developing or reproducing the software by the user are brought to
+ the user's attention, given its Free Software status, which may make it
+ complicated to use, with the result that its use is reserved for
+ developers and experienced professionals having in-depth computer
+ knowledge. Users are therefore encouraged to load and test the
+ suitability of the software as regards their requirements in conditions
+ enabling the security of their systems and/or data to be ensured and,
+ more generally, to use and operate it in the same conditions of
+ security. This Agreement may be freely reproduced and published,
+ provided it is not altered, and that no provisions are either added or
+ removed herefrom.
+ .
+ This Agreement may apply to any or all software for which the holder of
+ the economic rights decides to submit the use thereof to its provisions.
+ .
+ .
+     Article 1 - DEFINITIONS
+ .
+ For the purpose of this Agreement, when the following expressions
+ commence with a capital letter, they shall have the following meaning:
+ .
+ Agreement: means this license agreement, and its possible subsequent
+ versions and annexes.
+ .
+ Software: means the software in its Object Code and/or Source Code form
+ and, where applicable, its documentation, "as is" when the Licensee
+ accepts the Agreement.
+ .
+ Initial Software: means the Software in its Source Code and possibly its
+ Object Code form and, where applicable, its documentation, "as is" when
+ it is first distributed under the terms and conditions of the Agreement.
+ .
+ Modified Software: means the Software modified by at least one
+ Contribution.
+ .
+ Source Code: means all the Software's instructions and program lines to
+ which access is required so as to modify the Software.
+ .
+ Object Code: means the binary files originating from the compilation of
+ the Source Code.
+ .
+ Holder: means the holder(s) of the economic rights over the Initial
+ Software.
+ .
+ Licensee: means the Software user(s) having accepted the Agreement.
+ .
+ Contributor: means a Licensee having made at least one Contribution.
+ .
+ Licensor: means the Holder, or any other individual or legal entity, who
+ distributes the Software under the Agreement.
+ .
+ Contribution: means any or all modifications, corrections, translations,
+ adaptations and/or new functions integrated into the Software by any or
+ all Contributors, as well as any or all Internal Modules.
+ .
+ Module: means a set of sources files including their documentation that
+ enables supplementary functions or services in addition to those offered
+ by the Software.
+ .
+ External Module: means any or all Modules, not derived from the
+ Software, so that this Module and the Software run in separate address
+ spaces, with one calling the other when they are run.
+ .
+ Internal Module: means any or all Module, connected to the Software so
+ that they both execute in the same address space.
+ .
+ GNU GPL: means the GNU General Public License version 2 or any
+ subsequent version, as published by the Free Software Foundation Inc.
+ .
+ Parties: mean both the Licensee and the Licensor.
+ .
+ These expressions may be used both in singular and plural form.
+ .
+ .
+     Article 2 - PURPOSE
+ .
+ The purpose of the Agreement is the grant by the Licensor to the
+ Licensee of a non-exclusive, transferable and worldwide license for the
+ Software as set forth in Article 5 hereinafter for the whole term of the
+ protection granted by the rights over said Software.
+ .
+ .
+     Article 3 - ACCEPTANCE
+ .
+ 3.1 The Licensee shall be deemed as having accepted the terms and
+ conditions of this Agreement upon the occurrence of the first of the
+ following events:
+ .
+     * (i) loading the Software by any or all means, notably, by
+       downloading from a remote server, or by loading from a physical
+       medium;
+     * (ii) the first time the Licensee exercises any of the rights
+       granted hereunder.
+ .
+ 3.2 One copy of the Agreement, containing a notice relating to the
+ characteristics of the Software, to the limited warranty, and to the
+ fact that its use is restricted to experienced users has been provided
+ to the Licensee prior to its acceptance as set forth in Article 3.1
+ hereinabove, and the Licensee hereby acknowledges that it has read and
+ understood it.
+ .
+ .
+     Article 4 - EFFECTIVE DATE AND TERM
+ .
+ .
+       4.1 EFFECTIVE DATE
+ .
+ The Agreement shall become effective on the date when it is accepted by
+ the Licensee as set forth in Article 3.1.
+ .
+ .
+       4.2 TERM
+ .
+ The Agreement shall remain in force for the entire legal term of
+ protection of the economic rights over the Software.
+ .
+ .
+     Article 5 - SCOPE OF RIGHTS GRANTED
+ .
+ The Licensor hereby grants to the Licensee, who accepts, the following
+ rights over the Software for any or all use, and for the term of the
+ Agreement, on the basis of the terms and conditions set forth hereinafter.
+ .
+ Besides, if the Licensor owns or comes to own one or more patents
+ protecting all or part of the functions of the Software or of its
+ components, the Licensor undertakes not to enforce the rights granted by
+ these patents against successive Licensees using, exploiting or
+ modifying the Software. If these patents are transferred, the Licensor
+ undertakes to have the transferees subscribe to the obligations set
+ forth in this paragraph.
+ .
+ .
+       5.1 RIGHT OF USE
+ .
+ The Licensee is authorized to use the Software, without any limitation
+ as to its fields of application, with it being hereinafter specified
+ that this comprises:
+ .
+    1. permanent or temporary reproduction of all or part of the Software
+       by any or all means and in any or all form.
+ .
+    2. loading, displaying, running, or storing the Software on any or
+       all medium.
+ .
+    3. entitlement to observe, study or test its operation so as to
+       determine the ideas and principles behind any or all constituent
+       elements of said Software. This shall apply when the Licensee
+       carries out any or all loading, displaying, running, transmission
+       or storage operation as regards the Software, that it is entitled
+       to carry out hereunder.
+ .
+ .
+       5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
+ .
+ The right to make Contributions includes the right to translate, adapt,
+ arrange, or make any or all modifications to the Software, and the right
+ to reproduce the resulting software.
+ .
+ The Licensee is authorized to make any or all Contributions to the
+ Software provided that it includes an explicit notice that it is the
+ author of said Contribution and indicates the date of the creation thereof.
+ .
+ .
+       5.3 RIGHT OF DISTRIBUTION
+ .
+ In particular, the right of distribution includes the right to publish,
+ transmit and communicate the Software to the general public on any or
+ all medium, and by any or all means, and the right to market, either in
+ consideration of a fee, or free of charge, one or more copies of the
+ Software by any means.
+ .
+ The Licensee is further authorized to distribute copies of the modified
+ or unmodified Software to third parties according to the terms and
+ conditions set forth hereinafter.
+ .
+ .
+         5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
+ .
+ The Licensee is authorized to distribute true copies of the Software in
+ Source Code or Object Code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+    1. a copy of the Agreement,
+ .
+    2. a notice relating to the limitation of both the Licensor's
+       warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the Object Code of the Software is
+ redistributed, the Licensee allows future Licensees unhindered access to
+ the full Source Code of the Software by indicating how to access it, it
+ being understood that the additional cost of acquiring the Source Code
+ shall not exceed the cost of transferring the data.
+ .
+ .
+         5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
+ .
+ When the Licensee makes a Contribution to the Software, the terms and
+ conditions for the distribution of the resulting Modified Software
+ become subject to all the provisions of this Agreement.
+ .
+ The Licensee is authorized to distribute the Modified Software, in
+ source code or object code form, provided that said distribution
+ complies with all the provisions of the Agreement and is accompanied by:
+ .
+    1. a copy of the Agreement,
+ .
+    2. a notice relating to the limitation of both the Licensor's
+       warranty and liability as set forth in Articles 8 and 9,
+ .
+ and that, in the event that only the object code of the Modified
+ Software is redistributed, the Licensee allows future Licensees
+ unhindered access to the full source code of the Modified Software by
+ indicating how to access it, it being understood that the additional
+ cost of acquiring the source code shall not exceed the cost of
+ transferring the data.
+ .
+ .
+         5.3.3 DISTRIBUTION OF EXTERNAL MODULES
+ .
+ When the Licensee has developed an External Module, the terms and
+ conditions of this Agreement do not apply to said External Module, that
+ may be distributed under a separate license agreement.
+ .
+ .
+         5.3.4 COMPATIBILITY WITH THE GNU GPL
+ .
+ The Licensee can include a code that is subject to the provisions of one
+ of the versions of the GNU GPL in the Modified or unmodified Software,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ The Licensee can include the Modified or unmodified Software in a code
+ that is subject to the provisions of one of the versions of the GNU GPL,
+ and distribute that entire code under the terms of the same version of
+ the GNU GPL.
+ .
+ .
+     Article 6 - INTELLECTUAL PROPERTY
+ .
+ .
+       6.1 OVER THE INITIAL SOFTWARE
+ .
+ The Holder owns the economic rights over the Initial Software. Any or
+ all use of the Initial Software is subject to compliance with the terms
+ and conditions under which the Holder has elected to distribute its work
+ and no one shall be entitled to modify the terms and conditions for the
+ distribution of said Initial Software.
+ .
+ The Holder undertakes that the Initial Software will remain ruled at
+ least by this Agreement, for the duration set forth in Article 4.2.
+ .
+ .
+       6.2 OVER THE CONTRIBUTIONS
+ .
+ The Licensee who develops a Contribution is the owner of the
+ intellectual property rights over this Contribution as defined by
+ applicable law.
+ .
+ .
+       6.3 OVER THE EXTERNAL MODULES
+ .
+ The Licensee who develops an External Module is the owner of the
+ intellectual property rights over this External Module as defined by
+ applicable law and is free to choose the type of agreement that shall
+ govern its distribution.
+ .
+ .
+       6.4 JOINT PROVISIONS
+ .
+ The Licensee expressly undertakes:
+ .
+    1. not to remove, or modify, in any manner, the intellectual property
+       notices attached to the Software;
+ .
+    2. to reproduce said notices, in an identical manner, in the copies
+       of the Software modified or not.
+ .
+ The Licensee undertakes not to directly or indirectly infringe the
+ intellectual property rights of the Holder and/or Contributors on the
+ Software and to take, where applicable, vis--vis its staff, any and all
+ measures required to ensure respect of said intellectual property rights
+ of the Holder and/or Contributors.
+ .
+ .
+     Article 7 - RELATED SERVICES
+ .
+ 7.1 Under no circumstances shall the Agreement oblige the Licensor to
+ provide technical assistance or maintenance services for the Software.
+ .
+ However, the Licensor is entitled to offer this type of services. The
+ terms and conditions of such technical assistance, and/or such
+ maintenance, shall be set forth in a separate instrument. Only the
+ Licensor offering said maintenance and/or technical assistance services
+ shall incur liability therefor.
+ .
+ 7.2 Similarly, any Licensor is entitled to offer to its licensees, under
+ its sole responsibility, a warranty, that shall only be binding upon
+ itself, for the redistribution of the Software and/or the Modified
+ Software, under terms and conditions that it is free to decide. Said
+ warranty, and the financial terms and conditions of its application,
+ shall be subject of a separate instrument executed between the Licensor
+ and the Licensee.
+ .
+ .
+     Article 8 - LIABILITY
+ .
+ 8.1 Subject to the provisions of Article 8.2, the Licensee shall be
+ entitled to claim compensation for any direct loss it may have suffered
+ from the Software as a result of a fault on the part of the relevant
+ Licensor, subject to providing evidence thereof.
+ .
+ 8.2 The Licensor's liability is limited to the commitments made under
+ this Agreement and shall not be incurred as a result of in particular:
+ (i) loss due the Licensee's total or partial failure to fulfill its
+ obligations, (ii) direct or consequential loss that is suffered by the
+ Licensee due to the use or performance of the Software, and (iii) more
+ generally, any consequential loss. In particular the Parties expressly
+ agree that any or all pecuniary or business loss (i.e. loss of data,
+ loss of profits, operating loss, loss of customers or orders,
+ opportunity cost, any disturbance to business activities) or any or all
+ legal proceedings instituted against the Licensee by a third party,
+ shall constitute consequential loss and shall not provide entitlement to
+ any or all compensation from the Licensor.
+ .
+ .
+     Article 9 - WARRANTY
+ .
+ 9.1 The Licensee acknowledges that the scientific and technical
+ state-of-the-art when the Software was distributed did not enable all
+ possible uses to be tested and verified, nor for the presence of
+ possible defects to be detected. In this respect, the Licensee's
+ attention has been drawn to the risks associated with loading, using,
+ modifying and/or developing and reproducing the Software which are
+ reserved for experienced users.
+ .
+ The Licensee shall be responsible for verifying, by any or all means,
+ the suitability of the product for its requirements, its good working
+ order, and for ensuring that it shall not cause damage to either persons
+ or properties.
+ .
+ 9.2 The Licensor hereby represents, in good faith, that it is entitled
+ to grant all the rights over the Software (including in particular the
+ rights set forth in Article 5).
+ .
+ 9.3 The Licensee acknowledges that the Software is supplied "as is" by
+ the Licensor without any other express or tacit warranty, other than
+ that provided for in Article 9.2 and, in particular, without any warranty
+ as to its commercial value, its secured, safe, innovative or relevant
+ nature.
+ .
+ Specifically, the Licensor does not warrant that the Software is free
+ from any error, that it will operate without interruption, that it will
+ be compatible with the Licensee's own equipment and software
+ configuration, nor that it will meet the Licensee's requirements.
+ .
+ 9.4 The Licensor does not either expressly or tacitly warrant that the
+ Software does not infringe any third party intellectual property right
+ relating to a patent, software or any other property right. Therefore,
+ the Licensor disclaims any and all liability towards the Licensee
+ arising out of any or all proceedings for infringement that may be
+ instituted in respect of the use, modification and redistribution of the
+ Software. Nevertheless, should such proceedings be instituted against
+ the Licensee, the Licensor shall provide it with technical and legal
+ assistance for its defense. Such technical and legal assistance shall be
+ decided on a case-by-case basis between the relevant Licensor and the
+ Licensee pursuant to a memorandum of understanding. The Licensor
+ disclaims any and all liability as regards the Licensee's use of the
+ name of the Software. No warranty is given as regards the existence of
+ prior rights over the name of the Software or as regards the existence
+ of a trademark.
+ .
+ .
+     Article 10 - TERMINATION
+ .
+ 10.1 In the event of a breach by the Licensee of its obligations
+ hereunder, the Licensor may automatically terminate this Agreement
+ thirty (30) days after notice has been sent to the Licensee and has
+ remained ineffective.
+ .
+ 10.2 A Licensee whose Agreement is terminated shall no longer be
+ authorized to use, modify or distribute the Software. However, any
+ licenses that it may have granted prior to termination of the Agreement
+ shall remain valid subject to their having been granted in compliance
+ with the terms and conditions hereof.
+ .
+ .
+     Article 11 - MISCELLANEOUS
+ .
+ .
+       11.1 EXCUSABLE EVENTS
+ .
+ Neither Party shall be liable for any or all delay, or failure to
+ perform the Agreement, that may be attributable to an event of force
+ majeure, an act of God or an outside cause, such as defective
+ functioning or interruptions of the electricity or telecommunications
+ networks, network paralysis following a virus attack, intervention by
+ government authorities, natural disasters, water damage, earthquakes,
+ fire, explosions, strikes and labor unrest, war, etc.
+ .
+ 11.2 Any failure by either Party, on one or more occasions, to invoke
+ one or more of the provisions hereof, shall under no circumstances be
+ interpreted as being a waiver by the interested Party of its right to
+ invoke said provision(s) subsequently.
+ .
+ 11.3 The Agreement cancels and replaces any or all previous agreements,
+ whether written or oral, between the Parties and having the same
+ purpose, and constitutes the entirety of the agreement between said
+ Parties concerning said purpose. No supplement or modification to the
+ terms and conditions hereof shall be effective as between the Parties
+ unless it is made in writing and signed by their duly authorized
+ representatives.
+ .
+ 11.4 In the event that one or more of the provisions hereof were to
+ conflict with a current or future applicable act or legislative text,
+ said act or legislative text shall prevail, and the Parties shall make
+ the necessary amendments so as to comply with said act or legislative
+ text. All other provisions shall remain effective. Similarly, invalidity
+ of a provision of the Agreement, for any reason whatsoever, shall not
+ cause the Agreement as a whole to be invalid.
+ .
+ .
+       11.5 LANGUAGE
+ .
+ The Agreement is drafted in both French and English and both versions
+ are deemed authentic.
+ .
+ .
+     Article 12 - NEW VERSIONS OF THE AGREEMENT
+ .
+ 12.1 Any person is authorized to duplicate and distribute copies of this
+ Agreement.
+ .
+ 12.2 So as to ensure coherence, the wording of this Agreement is
+ protected and may only be modified by the authors of the License, who
+ reserve the right to periodically publish updates or new versions of the
+ Agreement, each with a separate number. These subsequent versions may
+ address new issues encountered by Free Software.
+ .
+ 12.3 Any Software distributed under a given version of the Agreement may
+ only be subsequently distributed under the same version of the Agreement
+ or a subsequent version, subject to the provisions of Article 5.3.4.
+ .
+ .
+     Article 13 - GOVERNING LAW AND JURISDICTION
+ .
+ 13.1 The Agreement is governed by French law. The Parties agree to
+ endeavor to seek an amicable solution to any disagreements or disputes
+ that may arise during the performance of the Agreement.
+ .
+ 13.2 Failing an amicable solution within two (2) months as from their
+ occurrence, and unless emergency proceedings are necessary, the
+ disagreements or disputes shall be referred to the Paris Courts having
+ jurisdiction, by the more diligent Party.
+ .
+ .
+ Version 2.0 dated 2006-09-05.
+ .
diff --git a/debian/patches/proper_soname.patch b/debian/patches/proper_soname.patch
new file mode 100644
index 0000000..62a2c57
--- /dev/null
+++ b/debian/patches/proper_soname.patch
@@ -0,0 +1,27 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 10 Sep 2016 23:41:37 +0200
+Description: Droping -release from LDFLAGS since otherwise a broken soname
+ is created
+
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -138,7 +138,7 @@ libGkArrays_ladir = @abs_srcdir@
+ libGkArrays_la_SOURCES = gkArrays.cpp solArray.cpp utils.cpp gkArraysBuilder.cpp gkSABuilder.cpp gkCFPSBuilder.cpp gkIFABuilder.cpp  readsReader.cpp largebinvect.cxx bitvector.cxx $(SUX_SRCS)
+ libGkArrays_la_configdir = @libdir@/@PACKAGE at -@VERSION@/include
+ libGkArrays_la_config_DATA = @abs_top_builddir@/config/config.h
+-libGkArrays_la_LDFLAGS = -version-info @LIB_VERSION@ -release @VERSION@ $(AM_LDFLAGS) # @LIBDIVSUFSORT@
++libGkArrays_la_LDFLAGS = -version-info @LIB_VERSION@ $(AM_LDFLAGS) # @LIBDIVSUFSORT@
+ 
+ if INCLUDED_PROGRESSBAR
+   AM_LDFLAGS += -L at abs_builddir@/libProgressBar-1.2.0/libProgressBar/.libs -lProgressBar
+--- a/src/libProgressBar-1.2.0/libProgressBar/Makefile.am
++++ b/src/libProgressBar-1.2.0/libProgressBar/Makefile.am
+@@ -4,7 +4,7 @@ lib_LTLIBRARIES = libProgressBar.la
+ libProgressBar_la_SOURCES = progressBar.h progressBar.cpp
+ libProgressBar_la_configdir = @libdir@/@PACKAGE at -@VERSION@/include
+ libProgressBar_la_config_DATA = config.h
+-libProgressBar_la_LDFLAGS = -version-info @LIB_VERSION@ -release @VERSION@ $(AM_LDFLAGS)
++libProgressBar_la_LDFLAGS = -version-info @LIB_VERSION@ $(AM_LDFLAGS)
+ 
+ noinst_PROGRAMS=testProgressBar
+ testProgressBar_SOURCES=testPB.cpp
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..e592159
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+proper_soname.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..deec47c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,33 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+VERSION        := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}' | sed -e 's/^[0-9]*://' -e 's/-.*//')
+
+%:
+	dh $@  --with autoreconf
+
+override_dh_install:
+	dh_install
+	rm -f debian/tmp/usr/include/libGkArrays-*/*.cxx
+	# find debian/tmp/usr/include -type l -delete
+	d-shlibmove --commit \
+		    --multiarch \
+		    --devunversioned \
+		    --exclude-la \
+		    --override s/libProgressBar0-dev/zlib1g-dev/ \
+		    --movedev debian/tmp/usr/include/libGkArrays-$(VERSION)/ usr/include \
+		    --movedev debian/tmp/usr/include/libProgressBar-1.2.0/ usr/include \
+		    --movedev debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/pkgconfig usr/lib/$(DEB_HOST_MULTIARCH) \
+		    debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libGkArrays.so
+	# now move libProgressBar manually
+	mv debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so.0* debian/libgkarrays1/usr/lib/$(DEB_HOST_MULTIARCH)
+	chmod -x debian/libgkarrays1/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so.0.*
+	mv debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.so debian/libgkarrays-dev/usr/lib/$(DEB_HOST_MULTIARCH)
+	mv debian/tmp/usr/lib/$(DEB_HOST_MULTIARCH)/libProgressBar.a debian/libgkarrays-dev/usr/lib/$(DEB_HOST_MULTIARCH)
+
+# the override is pure cheating since otherwise we's need to package zlib1g-dev separately
+#
+# d-shlibmove --commit --multiarch --devunversioned --override s/libProgressBar0-dev/libbpp-seq-dev/ debian/tmp/usr/lib/*/libGkArrays.so
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..6b7a678
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,10 @@
+Reference:
+  Author: Nicolas Philippe and Mikaël Salson and Thierry Lecroq and Martine Léonard and Thérèse Commes and Eric Rivals
+  Title: "Querying large read collections in main memory: a versatile data structure"
+  Journal: BMC Bioinformatics
+  Volume: 12
+  Pages: 242
+  Year: 2011
+  DOI: 10.1186/1471-2105-12-242
+  PMID: 21682852
+  URL: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-242
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..88f4260
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+http://gforge.inria.fr/frs/?group_id=3008 .*/libGkArrays-(.*)\.tar\.gz

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libgkarrays.git



More information about the debian-med-commit mailing list