[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


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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
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+         under
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+              requires that the Source form of the Modified Version, and of
+              any works derived from it, be made freely available in that
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+ 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
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+     provide new instructions on demand or cease further distribution. If you
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+     after you become aware that the instructions are invalid, then you do
+     not forfeit any of your rights under this license.
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+ (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.
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+ 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
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+      counterclaim) against any party alleging that the Package constitutes
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+
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

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