[med-svn] [r-bioc-genomeinfodbdata] 01/04: Initial packaging

Andreas Tille tille at debian.org
Fri Sep 29 11:15:51 UTC 2017


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tille pushed a commit to branch master
in repository r-bioc-genomeinfodbdata.

commit 57b8b9de371cb92381bef03fc8c31c24af6ba25e
Author: Graham Inggs <ginggs at debian.org>
Date:   Mon May 15 14:37:54 2017 +0000

    Initial packaging
---
 debian/README.source |  16 ++++++++
 debian/changelog     |   5 +++
 debian/compat        |   1 +
 debian/control       |  20 ++++++++++
 debian/copyright     | 106 +++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/rules         |   4 ++
 debian/source/format |   1 +
 debian/watch         |   3 ++
 8 files changed, 156 insertions(+)

diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..4ad890c
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,16 @@
+This package contains three mapping objects:
+
+* data/speciesMap.rda: A data frame with columns 'tax_id', 'genus', and
+  'species'.  Used to retrieve taxonomy ID by species and returns list of
+  available species.
+
+* data/validTaxIds.rda: An integer vector of valid taxonomy IDs created
+  from 'speciesMap'.  Used internally for quick taxonomy ID look ups.
+
+* data/specData.rds: A data frame with columns 'taxon' and 'species'.
+  Used internally to retrieve species by taxonomy ID.
+
+
+Scripts to generate these files are in inst/scripts.
+All originate from the public taxonomy dump at
+ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..17bd319
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-bioc-genomeinfodbdata (0.99.0-1) unstable; urgency=medium
+
+  * Initial release (Closes: #862550)
+
+ -- Graham Inggs <ginggs at debian.org>  Mon, 15 May 2017 16:12:39 +0200
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..f599e28
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+10
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..032a012
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,20 @@
+Source: r-bioc-genomeinfodbdata
+Section: gnu-r
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Graham Inggs <ginggs at debian.org>
+Build-Depends: debhelper (>= 10), dh-r, r-base-dev
+Standards-Version: 3.9.8
+Homepage: https://bioconductor.org/packages/GenomeInfoDbData/
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomeinfodbdata/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomeinfodbdata/trunk/
+
+Package: r-bioc-genomeinfodbdata
+Architecture: all
+Depends: ${R:Depends}, ${misc:Depends}, ${shlibs:Depends}
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
+Description: BioConductor species and taxonomy ID look up tables
+ This package contains files for mapping between NCBI taxonomy ID and species.
+ .
+ It is used by functions in the r-bioc-genomeinfodb package.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..b7e6571
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,106 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: GenomeInfoDbData
+Upstream-Contact: Bioconductor Maintainer <maintainer at bioconductor.org>
+Source: https://bioconductor.org/packages/GenomeInfoDbData/
+
+Files: *
+Copyright: 2006-2017 Sonali Arora, Martin Morgan, Marc Carlson, H. Pagès
+License: Artistic-2.0
+
+Files: debian/*
+Copyright: 2017 Graham Inggs <ginggs at debian.org>
+License: Artistic-2.0
+
+License: Artistic-2.0
+			 The "Artistic License"
+ .
+				Preamble
+ .
+ 1. You may make and give away verbatim copies of the source form of the
+    Standard Version of this Package without restriction, provided that
+    you duplicate all of the original copyright notices and associated
+    disclaimers.
+ .
+ 2. You may apply bug fixes, portability fixes and other modifications
+    derived from the Public Domain or from the Copyright Holder.  A
+    Package modified in such a way shall still be considered the Standard
+    Version.
+ .
+ 3. You may otherwise modify your copy of this Package in any way,
+    provided that you insert a prominent notice in each changed file stating
+    how and when you changed that file, and provided that you do at least
+    ONE of the following:
+ .
+    a) place your modifications in the Public Domain or otherwise make them
+    Freely Available, such as by posting said modifications to Usenet or
+    an equivalent medium, or placing the modifications on a major archive
+    site such as uunet.uu.net, or by allowing the Copyright Holder to include
+    your modifications in the Standard Version of the Package.
+ .
+    b) use the modified Package only within your corporation or organization.
+ .
+    c) rename any non-standard executables so the names do not conflict
+    with standard executables, which must also be provided, and provide
+    a separate manual page for each non-standard executable that clearly
+    documents how it differs from the Standard Version.
+ .
+    d) make other distribution arrangements with the Copyright Holder.
+ .
+ 4. You may distribute the programs of this Package in object code or
+    executable form, provided that you do at least ONE of the following:
+ .
+    a) distribute a Standard Version of the executables and library files,
+    together with instructions (in the manual page or equivalent) on where
+    to get the Standard Version.
+ .
+    b) accompany the distribution with the machine-readable source of
+    the Package with your modifications.
+ .
+    c) give non-standard executables non-standard names, and clearly
+    document the differences in manual pages (or equivalent), together
+    with instructions on where to get the Standard Version.
+ .
+    d) make other distribution arrangements with the Copyright Holder.
+ .
+ 5. You may charge a reasonable copying fee for any distribution of this
+    Package.  You may charge any fee you choose for support of this Package.
+    You may not charge a fee for this Package itself.  However, you may
+    distribute this Package in aggregate with other (possibly commercial)
+    programs as part of a larger (possibly commercial) software distribution
+    provided that you do not advertise this Package as a product of your
+    own.  You may embed this Package's interpreter within an executable of
+    yours (by linking); this shall be construed as a mere form of
+    aggregation, provided that the complete Standard Version of the
+    interpreter is so embedded.
+ .
+ 6. The scripts and library files supplied as input to or produced as
+    output from the programs of this Package do not automatically fall under
+    the copyright of this Package, but belong to whoever generated them, and
+    may be sold commercially, and may be aggregated with this Package.  If
+    such scripts or library files are aggregated with this Package via the
+    so-called "undump" or "unexec" methods of producing a binary executable
+    image, then distribution of such an image shall neither be construed as
+    a distribution of this Package nor shall it fall under the restrictions
+    of Paragraphs 3 and 4, provided that you do not represent such an
+    executable image as a Standard Version of this Package.
+ .
+ 7. C subroutines (or comparably compiled subroutines in other
+    languages) supplied by you and linked into this Package in order to
+    emulate subroutines and variables of the language defined by this
+    Package shall not be considered part of this Package, but are the
+    equivalent of input as in Paragraph 6, provided these subroutines do
+    not change the language in any way that would cause it to fail the
+    regression tests for the language.
+ .
+ 8. Aggregation of this Package with a commercial distribution is always
+    permitted provided that the use of this Package is embedded; that is,
+    when no overt attempt is made to make this Package's interfaces visible
+    to the end user of the commercial distribution.  Such use shall not be
+    construed as a distribution of this Package.
+ .
+ 9. The name of the Copyright Holder may not be used to endorse or promote
+    products derived from this software without specific prior written permission.
+ .
+ 10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR
+    IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED
+    WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..68d9a36
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+%:
+	dh $@ --buildsystem R
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..9248da7
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=4
+opts=downloadurlmangle=s?^(.*)\.\.?https:$1packages/release/data/annotation? \
+http://www.bioconductor.org/packages/release/data/annotation/html/GenomeInfoDbData.html .*/GenomeInfoDbData_(.*).tar.gz

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