--- r-bioc-biobase-2.14.0.orig/debian/watch +++ r-bioc-biobase-2.14.0/debian/watch @@ -0,0 +1,5 @@ +version=3 + +# This tracks the current stable version of bioconductor +http://www.bioconductor.org/help/bioc-views/release/bioc/html/Biobase.html \ + /packages/.*/bioc/src/contrib/Biobase_(.*).tar.gz --- r-bioc-biobase-2.14.0.orig/debian/control +++ r-bioc-biobase-2.14.0/debian/control @@ -0,0 +1,33 @@ +Source: r-bioc-biobase +Section: gnu-r +Priority: optional +Maintainer: Debian Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Charles Plessy +Build-Depends: cdbs, debhelper (>= 8), r-base-dev (>= 2.10) +Standards-Version: 3.9.2 +Vcs-Browser: http://git.debian.org/?p=debian-med/r-bioc-biobase.git +Vcs-Git: git://git.debian.org/git/debian-med/r-bioc-biobase.git +Homepage: http://www.bioconductor.org + +Package: r-bioc-biobase +Architecture: any +# Keep until Ubuntu LTS 12.4 +Pre-Depends: dpkg (>= 1.15.6) +Depends: ${shlibs:Depends}, ${misc:Depends}, ${R:Depends} +Description: base functions for Bioconductor + Biobase is part of the Bioconductor project, and is used by many other + packages. Biobase contains standardized data structures to represent genomic + data, and functions that are needed by many other packages or which replace R + functions. + . + Bioconductor is a project to develop innovative software tools for use in + computational biology. It is based on the R language. You should already be + quite familiar with R before using Bioconductor. Bioconductor packages provide + flexible interactive tools for carrying out a number of different computational + tasks. + . + Most other Bioconductor packages are not packaged for Debian, but this + packages provides in its Debian documentation instructions on how to install + unofficial auto-generated Bioconductor packages for Debian and Ubuntu systems, + that are prepared by members of the Debian Med team. --- r-bioc-biobase-2.14.0.orig/debian/changelog +++ r-bioc-biobase-2.14.0/debian/changelog @@ -0,0 +1,20 @@ +r-bioc-biobase (2.14.0-1) unstable; urgency=low + + [cb6b786] Bioconductor release 2.9. + [d70e490] Build-Depend on R >= 2.10 according to DESCRIPTION. + [ae99e35] Include 7 digits of the commit id in the changelog entry. + [33b5d47] Compress binary package with xz. + + -- Charles Plessy Wed, 02 Nov 2011 13:52:04 +0900 + +r-bioc-biobase (2.12.2-1) unstable; urgency=low + + * New upstream release. + + -- Charles Plessy Thu, 04 Aug 2011 08:58:03 +0900 + +r-bioc-biobase (2.12.1-1) unstable; urgency=low + + * Initial release (Closes: #169859) + + -- Charles Plessy Sat, 14 May 2011 22:35:11 +0900 --- r-bioc-biobase-2.14.0.orig/debian/docs +++ r-bioc-biobase-2.14.0/debian/docs @@ -0,0 +1 @@ +NEWS --- r-bioc-biobase-2.14.0.orig/debian/copyright +++ r-bioc-biobase-2.14.0/debian/copyright @@ -0,0 +1,221 @@ +Format: http://dep.debian.net/deps/dep5/ +Source: http://www.bioconductor.org/packages/2.9/bioc/src/contrib/Biobase_2.14.0.tar.gz + +Files: * +Copyright: none claimed, but an author list is provided in the DESCRIPTION file. +License: Artistic-2.0 + + +Files: src/rowMedians.c src/anyMissing.c +Copyright: © Henrik Bengtsson, 2007 +License: Artistic-2.0 +Comment: Copies from the CRAN matrixStats packages, see: + http://cran.r-project.org/web/packages/matrixStats + + +Files: src/envir.c +Copyright: © R. Gentleman, 2003 +License: Artistic-2.0 +Comment: R. Gentleman is listed as author in the DESCRIPTION file. + + +Files: debian/* +Copyright: © 2011, Charles Plessy +License: BOLA-1.1 + BOLA - Buena Onda License Agreement (v1.1) + ------------------------------------------ + . + This work is provided 'as-is', without any express or implied warranty. In no + event will the authors be held liable for any damages arising from the use of + this work. + . + To all effects and purposes, this work is to be considered Public Domain. + . + . + However, if you want to be "buena onda", you should: + . + 1. Not take credit for it, and give proper recognition to the authors. + 2. Share your modifications, so everybody benefits from them. + 3. Do something nice for the authors. + 4. Help someone who needs it: sign up for some volunteer work or help your + neighbour paint the house. + 5. Don't waste. Anything, but specially energy that comes from natural + non-renewable resources. Extra points if you discover or invent something + to replace them. + 6. Be tolerant. Everything that's good in nature comes from cooperation. + + +License: Artistic-2.0 + Copyright (c) 2000-2006, The Perl Foundation. + . + Everyone is permitted to copy and distribute verbatim copies of this license + document, but changing it is not allowed. + . + . + Preamble + This license establishes the terms under which a given free software Package may + be copied, modified, distributed, and/or redistributed. The intent is that the + Copyright Holder maintains some artistic control over the development of that + Package while still keeping the Package available as open source and free + software. + . + You are always permitted to make arrangements wholly outside of this license + directly with the Copyright Holder of a given Package. If the terms of this + license do not permit the full use that you propose to make of the Package, you + should contact the Copyright Holder and seek a different licensing arrangement. + . + . + Definitions + "Copyright Holder" means the individual(s) or organization(s) named in the + copyright notice for the entire Package. + . + "Contributor" means any party that has contributed code or other material to the + Package, in accordance with the Copyright Holder's procedures. + . + "You" and "your" means any person who would like to copy, distribute, or modify + the Package. + . + "Package" means the collection of files distributed by the Copyright Holder, and + derivatives of that collection and/or of those files. A given Package may + consist of either the Standard Version, or a Modified Version. + . + "Distribute" means providing a copy of the Package or making it accessible to + anyone else, or in the case of a company or organization, to others outside of + your company or organization. + . + "Distributor Fee" means any fee that you charge for Distributing this Package or + providing support for this Package to another party. It does not mean licensing + fees. + . + "Standard Version" refers to the Package if it has not been modified, or has + been modified only in ways explicitly requested by the Copyright Holder. + . + "Modified Version" means the Package, if it has been changed, and such changes + were not explicitly requested by the Copyright Holder. + . + "Original License" means this Artistic License as Distributed with the Standard + Version of the Package, in its current version or as it may be modified by The + Perl Foundation in the future. + . + "Source" form means the source code, documentation source, and configuration + files for the Package. + . + "Compiled" form means the compiled bytecode, object code, binary, or any other + form resulting from mechanical transformation or translation of the Source form. + . + . + Permission for Use and Modification Without Distribution + (1) You are permitted to use the Standard Version and create and use Modified + Versions for any purpose without restriction, provided that you do not + Distribute the Modified Version. + . + . + Permissions for Redistribution of the Standard Version + (2) You may Distribute verbatim copies of the Source form of the Standard + Version of this Package in any medium without restriction, either gratis or for + a Distributor Fee, provided that you duplicate all of the original copyright + notices and associated disclaimers. At your discretion, such verbatim copies may + or may not include a Compiled form of the Package. + . + (3) You may apply any bug fixes, portability changes, and other modifications + made available from the Copyright Holder. The resulting Package will still be + considered the Standard Version, and as such will be subject to the Original + License. + . + . + Distribution of Modified Versions of the Package as Source + (4) You may Distribute your Modified Version as Source (either gratis or for a + Distributor Fee, and with or without a Compiled form of the Modified Version) + provided that you clearly document how it differs from the Standard Version, + including, but not limited to, documenting any non-standard features, + executables, or modules, and provided that you do at least ONE of the + following: + . + (a) make the Modified Version available to the Copyright Holder of the Standard + Version, under the Original License, so that the Copyright Holder may include + your modifications in the Standard Version. + . + (b) ensure that installation of your Modified Version does not prevent the user + installing or running the Standard Version. In addition, the Modified Version + must bear a name that is different from the name of the Standard Version. + . + (c) allow anyone who receives a copy of the Modified Version to make the Source + form of the Modified Version available to others under + . + (i) the Original License or + . + (ii) a license that permits the licensee to freely copy, modify and redistribute + the Modified Version using the same licensing terms that apply to the copy that + the licensee received, and requires that the Source form of the Modified + Version, and of any works derived from it, be made freely available in that + license fees are prohibited but Distributor Fees are allowed. + . + Distribution of Compiled Forms of the Standard Version or Modified Versions without the Source + . + (5) You may Distribute Compiled forms of the Standard Version without the + Source, provided that you include complete instructions on how to get the + Source of the Standard Version. Such instructions must be valid at the time of + your distribution. If these instructions, at any time while you are carrying out + such distribution, become invalid, you must provide new instructions on demand + or cease further distribution. If you provide valid instructions or cease + distribution within thirty days after you become aware that the instructions are + invalid, then you do not forfeit any of your rights under this license. + . + (6) You may Distribute a Modified Version in Compiled form without the Source, + provided that you comply with Section 4 with respect to the Source of the + Modified Version. + . + . + Aggregating or Linking the Package + (7) You may aggregate the Package (either the Standard Version or Modified + Version) with other packages and Distribute the resulting aggregation provided + that you do not charge a licensing fee for the Package. Distributor Fees are + permitted, and licensing fees for other components in the aggregation are + permitted. The terms of this license apply to the use and Distribution of the + Standard or Modified Versions as included in the aggregation. + . + (8) You are permitted to link Modified and Standard Versions with other works, + to embed the Package in a larger work of your own, or to build stand-alone + binary or bytecode versions of applications that include the Package, and + Distribute the result without restriction, provided the result does not expose a + direct interface to the Package. + . + . + Items That are Not Considered Part of a Modified Version + (9) Works (including, but not limited to, modules and scripts) that merely + extend or make use of the Package, do not, by themselves, cause the Package to + be a Modified Version. In addition, such works are not considered parts of the + Package itself, and are not subject to the terms of this license. + . + . + General Provisions + (10) Any use, modification, and distribution of the Standard or Modified + Versions is governed by this Artistic License. By using, modifying or + distributing the Package, you accept this license. Do not use, modify, or + distribute the Package, if you do not accept this license. + . + (11) If your Modified Version has been derived from a Modified Version made by + someone other than you, you are nevertheless required to ensure that your + Modified Version complies with the requirements of this license. + . + (12) This license does not grant you the right to use any trademark, service + mark, tradename, or logo of the Copyright Holder. + . + (13) This license includes the non-exclusive, worldwide, free-of-charge patent + license to make, have made, use, offer to sell, sell, import and otherwise + transfer the Package with respect to any patent claims licensable by the + Copyright Holder that are necessarily infringed by the Package. If you institute + patent litigation (including a cross-claim or counterclaim) against any party + alleging that the Package constitutes direct or contributory patent + infringement, then this Artistic License to you shall terminate on the date that + such litigation is filed. + . + (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND + CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED + WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR + NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW. + UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR + ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY + OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH + DAMAGE. + --- r-bioc-biobase-2.14.0.orig/debian/gbp.conf +++ r-bioc-biobase-2.14.0/debian/gbp.conf @@ -0,0 +1,9 @@ +# This package is managed with git-buildpackage. + +[DEFAULT] +# use pristine-tar: +pristine-tar = True + +[git-dch] +# include 7 digits of the commit id in the changelog enty: +id-length = 7 --- r-bioc-biobase-2.14.0.orig/debian/README.Debian +++ r-bioc-biobase-2.14.0/debian/README.Debian @@ -0,0 +1,6 @@ +Unofficial auto-built Bioconductor packages for Debian and Ubuntu +───────────────────────────────────────────────────────────────── + +The documentation is being written. In the meantime, please refer to: + +http://lists.debian.org/debian-med/2011/02/msg00202.html --- r-bioc-biobase-2.14.0.orig/debian/rules +++ r-bioc-biobase-2.14.0/debian/rules @@ -0,0 +1,10 @@ +#!/usr/bin/make -f + +debRreposname = bioc +include /usr/share/R/debian/r-cran.mk + +DEB_DH_BUILDDEB_ARGS := -- -Z xz + +# Require a number equal or superior than the R version the package was built with. +install/r-$(debRreposname)-$(cranName):: + echo "R:Depends=r-base-core (>= $(shell R --version | head -n1 | perl -ne 'print / +([0-9]\.[0-9]+\.[0-9])/')~)" >> debian/r-$(debRreposname)-$(cranName).substvars --- r-bioc-biobase-2.14.0.orig/debian/compat +++ r-bioc-biobase-2.14.0/debian/compat @@ -0,0 +1 @@ +8