[med-svn] r15792 - in trunk/packages/R: . r-bioc-hgu95av2.db r-bioc-hgu95av2.db/trunk r-bioc-hgu95av2.db/trunk/debian r-bioc-hgu95av2.db/trunk/debian/source

Andreas Tille tille at moszumanska.debian.org
Thu Jan 16 14:54:32 UTC 2014


Author: tille
Date: 2014-01-16 14:54:32 +0000 (Thu, 16 Jan 2014)
New Revision: 15792

Added:
   trunk/packages/R/r-bioc-hgu95av2.db/
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/README.test
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/changelog
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/compat
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/control
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/copyright
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/rules
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/source/
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/source/format
   trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/watch
Log:
If we want to run r-bioc-annotationdbi successfully we need hgu95av2.db ... but this in turn needs org.Hs.eg.db; starting again fighting trough BioConductor dependencies


Added: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/README.test	2014-01-16 14:54:32 UTC (rev 15792)
@@ -0,0 +1,5 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by loading it into R with the command
+‘library()’ in order to confirm its integrity.

Added: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/changelog	2014-01-16 14:54:32 UTC (rev 15792)
@@ -0,0 +1,6 @@
+r-bioc-hgu95av2.db (2.10.1-1) UNRELEASED; urgency=low
+
+  * Initial release (closes: #???)
+  TODO: Depends: org.Hs.eg.db which needs to be packaged
+
+ -- Andreas Tille <tille at debian.org>  Thu, 16 Jan 2014 14:13:14 +0100

Added: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/compat	2014-01-16 14:54:32 UTC (rev 15792)
@@ -0,0 +1 @@
+9

Added: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/control	2014-01-16 14:54:32 UTC (rev 15792)
@@ -0,0 +1,23 @@
+Source: r-bioc-hgu95av2.db
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               cdbs,
+               r-base-dev,
+               r-bioc-annotationdbi
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-hgu95av2.db/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-hgu95av2.db/trunk/
+Homepage: http://www.bioconductor.org/packages/release/data/annotation/html/hgu95av2.db.html
+
+Package: r-bioc-hgu95av2.db
+Architecture: all
+Depends: ${R:Depends},
+         ${misc:Depends},
+         r-bioc-annotationdbi
+Description: Affymetrix Human Genome U95 Set annotation data (chip hgu95av2)
+ This package is part of BioConductor and provides Affymetrix Human
+ Genome U95 Set annotation data (chip hgu95av2) assembled using data from
+ public repositories.

Added: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/copyright	2014-01-16 14:54:32 UTC (rev 15792)
@@ -0,0 +1,134 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: hgu95av2.db
+Upstream-Contact: Bioconductor Package Maintainer <maintainer at bioconductor.org> 
+Source: http://www.bioconductor.org/packages/release/data/annotation/html/hgu95av2.db.html
+
+Files: *
+Copyright: © 2006-2013 Marc Carlson 
+License: Artistic-2.0
+
+Files: debian/*
+Copyright: 2014 Andreas Tille <tille at debian.org>
+License: Artistic-2.0
+
+License: Artistic-2.0
+ 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.
+

Added: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/rules	2014-01-16 14:54:32 UTC (rev 15792)
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+debRreposname=bioc
+include /usr/share/R/debian/r-cran.mk


Property changes on: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/source/format	2014-01-16 14:54:32 UTC (rev 15792)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/R/r-bioc-hgu95av2.db/trunk/debian/watch	2014-01-16 14:54:32 UTC (rev 15792)
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s/\.\./packages\/release\/data\/annotation/ \
+ http://www.bioconductor.org/packages/release/data/annotation/html/hgu95av2.db.html .*/hgu95av2\.db_([\d\.]+)\.tar\.gz




More information about the debian-med-commit mailing list