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debian/changelog
View file @ 1ffef5be
biococoa (2.2.2-4) unstable; urgency=medium
* Drop unneeded get-orig-source target
* DEP5
* debhelper 10
(dh_systemd_enable is no longer used in compat >= 11, please use
dh_installsystemd instead -> that's a cdbs issue)
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
-- Andreas Tille <tille@debian.org> Tue, 09 Oct 2018 16:25:32 +0200
biococoa (2.2.2-3) unstable; urgency=medium
* Moved packaging from SVN to Git
......
debian/control
View file @ 1ffef5be
......@@ -7,11 +7,11 @@ Section: science
Priority: optional
Build-Depends: cdbs,
gnustep-make,
debhelper (>= 9),
debhelper (>= 11~),
libgnustep-base-dev
Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/biococoa.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/biococoa.git
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/biococoa
Vcs-Git: https://salsa.debian.org/med-team/biococoa.git
Homepage: http://bioinformatics.org/biococoa/
Package: libbiococoa-dev
......
debian/copyright
View file @ 1ffef5be
This package was debianized by Gürkan Sengün <gurkan@linuks.mine.nu> on
Tue, 21 Dec 2004 00:30:09 +0100.
It was downloaded from http://bioinformatics.org/biococoa/
Upstream Author: Scott Christley <schristley@mac.com>
Upstream Author: Peter Schols <peter.schols@bio.kuleuven.ac.be>
Copyright:
Copyright (c) 2003-2009 The BioCocoa Project.
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. The name of the author may not be used to endorse or promote products
derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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.
Portions of BioCocoa covered by other licenses
==============================================
Hybrid suffix-array builder, written by Sean Quinlan and Sean Doward,
distributed under the Lucent Public License Version 1.02.
Copyright (C) 2003, Lucent Technologies Inc. and others. All Rights Reserved.
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: BioCocoa
Source: http://bioinformatics.org/biococoa/downloads/
Files: *
Copyright: 2003-2010 Scott Christley <schristley@mac.com>,
Peter Schols <peter.schols@bio.kuleuven.ac.be>,
The BioCocoa Project.
License: BSD-3-Clause
Files: debian/*
Copyright: 2004 Gürkan Sengün <gurkan@linuks.mine.nu> on
License: BSD-3-Clause
Files: BCFoundation/BCAnalysis/BCSuffixArray.*
Copyright: 2003, Sean Quinlan and Sean Doward,
Lucent Technologies Inc. and others
License: LPL-1.02
Lucent Public License Version 1.02.
.
THE ACCOMPANYING PROGRAM IS PROVIDED UNDER THE TERMS OF THIS PUBLIC
LICENSE ("AGREEMENT"). ANY USE, REPRODUCTION OR DISTRIBUTION OF THE
PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT.
.
1. DEFINITIONS
.
"Contribution" means:
.
1. in the case of Lucent Technologies Inc. ("LUCENT"), the Original
Program, and
2. in the case of each Contributor,
......@@ -60,36 +36,36 @@ PROGRAM CONSTITUTES RECIPIENT'S ACCEPTANCE OF THIS AGREEMENT.
Contributor's behalf, and the Contributor explicitly consents,
in accordance with Section 3C, to characterization of the
changes and/or additions as Contributions.
.
"Contributor" means LUCENT and any other entity that has Contributed
a Contribution to the Program.
.
"Distributor" means a Recipient that distributes the Program,
modifications to the Program, or any part thereof.
.
"Licensed Patents" mean patent claims licensable by a Contributor
which are necessarily infringed by the use or sale of its Contribution
alone or when combined with the Program.
.
"Original Program" means the original version of the software
accompanying this Agreement as released by LUCENT, including source
code, object code and documentation, if any.
.
"Program" means the Original Program and Contributions or any part
thereof
.
"Recipient" means anyone who receives the Program under this
Agreement, including all Contributors.
.
2. GRANT OF RIGHTS
.
a. Subject to the terms of this Agreement, each Contributor hereby
grants Recipient a non-exclusive, worldwide, royalty-free copyright
license to reproduce, prepare derivative works of, publicly display,
publicly perform, distribute and sublicense the Contribution of such
Contributor, if any, and such derivative works, in source code and
object code form.
.
b. Subject to the terms of this Agreement, each Contributor hereby
grants Recipient a non-exclusive, worldwide, royalty-free patent
license under Licensed Patents to make, use, sell, offer to sell,
......@@ -103,7 +79,7 @@ Agreement, including all Contributors.
to (i) any other combinations which include the Contribution, nor to
(ii) Contributions of other Contributors. No hardware per se is
licensed hereunder.
.
c. Recipient understands that although each Contributor grants the
licenses to its Contributions set forth herein, no assurances are
provided by any Contributor that the Program does not infringe the
......@@ -117,54 +93,54 @@ Agreement, including all Contributors.
third party patent license is required to allow Recipient to
distribute the Program, it is Recipient's responsibility to acquire
that license before distributing the Program.
.
d. Each Contributor represents that to its knowledge it has
sufficient copyright rights in its Contribution, if any, to grant
the copyright license set forth in this Agreement.
.
3. REQUIREMENTS
.
A. Distributor may choose to distribute the Program in any form under
this Agreement or under its own license agreement, provided that:
.
1. it complies with the terms and conditions of this Agreement;
.
2. if the Program is distributed in source code or other tangible
form, a copy of this Agreement or Distributor's own license
agreement is included with each copy of the Program; and
.
3. if distributed under Distributor's own license agreement, such
license agreement:
.
1. effectively disclaims on behalf of all Contributors all
warranties and conditions, express and implied, including
warranties or conditions of title and non-infringement, and
implied warranties or conditions of merchantability and
fitness for a particular purpose;
.
2. effectively excludes on behalf of all Contributors all
liability for damages, including direct, indirect, special,
incidental and consequential damages, such as lost profits;
and
.
3. states that any provisions which differ from this
Agreement are offered by that Contributor alone and not by
any other party.
.
B. Each Distributor must include the following in a conspicuous
location in the Program:
.
Copyright (C) 2003, Lucent Technologies Inc. and others. All Rights Reserved.
.
C. In addition, each Contributor must identify itself as the
originator of its Contribution in a manner that reasonably allows
subsequent Recipients to identify the originator of the
Contribution. Also, each Contributor must agree that the additions
and/or changes are intended to be a Contribution. Once a Contribution
is contributed, it may not thereafter be revoked.
.
4. COMMERCIAL DISTRIBUTION
.
Commercial distributors of software may accept certain
responsibilities with respect to end users, business partners and the
like. While this license is intended to facilitate the commercial use
......@@ -187,7 +163,7 @@ and b) allow the Commercial Distributor to control, and cooperate with
the Commercial Distributor in, the defense and any related settlement
negotiations. The Indemnified Contributor may participate in any such
claim at its own expense.
.
For example, a Distributor might include the Program in a commercial
product offering, Product X. That Distributor is then a Commercial
Distributor. If that Commercial Distributor then makes performance
......@@ -198,9 +174,9 @@ defend claims against the Contributors related to those performance
claims and warranties, and if a court requires any Contributor to pay
any damages as a result, the Commercial Distributor must pay those
damages.
.
5. NO WARRANTY
.
EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, THE PROGRAM IS
PROVIDED ON AN "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
KIND, EITHER EXPRESS OR IMPLIED INCLUDING, WITHOUT LIMITATION, ANY
......@@ -212,9 +188,9 @@ exercise of rights under this Agreement, including but not limited to
the risks and costs of program errors, compliance with applicable
laws, damage to or loss of data, programs or equipment, and
unavailability or interruption of operations.
.
6. DISCLAIMER OF LIABILITY
.
EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT, NEITHER RECIPIENT NOR
ANY CONTRIBUTORS SHALL HAVE ANY LIABILITY FOR ANY DIRECT, INDIRECT,
INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING
......@@ -223,21 +199,21 @@ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OR
DISTRIBUTION OF THE PROGRAM OR THE EXERCISE OF ANY RIGHTS GRANTED
HEREUNDER, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.
.
7. EXPORT CONTROL
.
Recipient agrees that Recipient alone is responsible for compliance
with the United States export administration regulations (and the
export control laws and regulation of any other countries).
.
8. GENERAL
.
If any provision of this Agreement is invalid or unenforceable under
applicable law, it shall not affect the validity or enforceability of
the remainder of the terms of this Agreement, and without further
action by the parties hereto, such provision shall be reformed to the
minimum extent necessary to make such provision valid and enforceable.
.
If Recipient institutes patent litigation against a Contributor with
respect to a patent applicable to software (including a cross-claim or
counterclaim in a lawsuit), then any patent licenses granted by that
......@@ -249,7 +225,7 @@ itself (excluding combinations of the Program with other software or
hardware) infringes such Recipient's patent(s), then such Recipient's
rights granted under Section 2(b) shall terminate as of the date such
litigation is filed.
.
All Recipient's rights under this Agreement shall terminate if it
fails to comply with any of the material terms or conditions of this
Agreement and does not cure such failure in a reasonable period of
......@@ -259,7 +235,7 @@ and distribution of the Program as soon as reasonably
practicable. However, Recipient's obligations under this Agreement and
any licenses granted by Recipient relating to the Program shall
continue and survive.
.
LUCENT may publish new versions (including revisions) of this
Agreement from time to time. Each new version of the Agreement will be
given a distinguishing version number. The Program (including
......@@ -273,9 +249,32 @@ Recipient receives no rights or licenses to the intellectual property
of any Contributor under this Agreement, whether expressly, by
implication, estoppel or otherwise. All rights in the Program not
expressly granted under this Agreement are reserved.
.
This Agreement is governed by the laws of the State of New York and
the intellectual property laws of the United States of America. No
party to this Agreement will bring a legal action under this Agreement
more than one year after the cause of action arose. Each party waives
its rights to a jury trial in any resulting litigation.
License: BSD-3-Clause
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. The name of the author may not be used to endorse or promote products
derived from this software without specific prior written permission.
.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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.
debian/rules
View file @ 1ffef5be
......@@ -31,12 +31,3 @@ else
OPTFLAG := -O2
endif
DEB_MAKE_INVOKE += OPTFLAG=$(OPTFLAG)
#binary-post-install/libbiococoa-dev::
# find $(d_dev)/usr/share/doc/$(DEB_GS_DEVPKG_NAME_$(framework))/examples/ \
# -type f -exec chmod 644 \{\} \;
get-orig-source:
mkdir -p ../tarballs
uscan --verbose --force-download --destdir=../tarballs