[med-svn] [r-bioc-bsgenome.hsapiens.ucsc.hg19] 01/03: BioC people said that this data set is needed to run the test suite of rtracklayers. While I have doubt about this I simply try while it is not intended to really upload this as Debian package
Andreas Tille
tille at debian.org
Thu Nov 9 12:39:54 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-bsgenome.hsapiens.ucsc.hg19.
commit ce4a3935ad0e3b743d4abc2ab00a0520d793594a
Author: Andreas Tille <tille at debian.org>
Date: Fri Aug 8 09:37:37 2014 +0000
BioC people said that this data set is needed to run the test suite of rtracklayers. While I have doubt about this I simply try while it is not intended to really upload this as Debian package
---
debian/README.test | 5 ++
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 24 +++++++++
debian/copyright | 134 +++++++++++++++++++++++++++++++++++++++++++++++++++
debian/rules | 4 ++
debian/source/format | 1 +
debian/watch | 3 ++
8 files changed, 177 insertions(+)
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..de7ed1e
--- /dev/null
+++ b/debian/README.test
@@ -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(BSgenome.Hsapiens.UCSC.hg19)’ in order to confirm its integrity.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..28957ba
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-bioc-bsgenome.hsapiens.ucsc.hg19 (1.3.1000-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Fri, 08 Aug 2014 11:31:46 +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..929195e
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: r-bioc-bsgenome.hsapiens.ucsc.hg19
+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,
+ r-bioc-genomicfeatures
+Standards-Version: 3.9.5
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-bsgenome.hsapiens.ucsc.hg19/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-bsgenome.hsapiens.ucsc.hg19/trunk/
+Homepage: http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html
+
+Package: r-bioc-bsgenome.hsapiens.ucsc.hg19
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-bioc-annotationdbi,
+ r-bioc-genomicfeatures
+Description: Full genome sequences for Homo sapiens (UCSC version hg19)
+ Full genome sequences for Homo sapiens (Human) as provided by UCSC
+ (hg19, Feb. 2009) and stored in Biostrings objects.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..88a166d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,134 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: BSgenome.Hsapiens.UCSC.hg19
+Upstream-Contact: Bioconductor Package Maintainer <maintainer at bioconductor.org>
+Source: http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html
+
+Files: *
+Copyright: © 2006-2014 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.
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..aeb12b3
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+debRreposname=bioc
+include /usr/share/R/debian/r-cran.mk
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/watch b/debian/watch
new file mode 100644
index 0000000..e5d218e
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s/\.\./packages\/release\/data\/annotation/ \
+ http://www.bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html .*/BSgenome\.Hsapiens\.UCSC\.hg19_([\d\.]+)\.tar\.gz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-bsgenome.hsapiens.ucsc.hg19.git
More information about the debian-med-commit
mailing list