[med-svn] r22728 - in trunk/packages/R/r-bioc-biomformat/trunk: . debian debian/patches debian/source debian/tests
Andreas Tille
tille at moszumanska.debian.org
Sat Aug 27 08:54:09 UTC 2016
Author: tille
Date: 2016-08-27 08:54:08 +0000 (Sat, 27 Aug 2016)
New Revision: 22728
Added:
trunk/packages/R/r-bioc-biomformat/trunk/debian/
trunk/packages/R/r-bioc-biomformat/trunk/debian/README.test
trunk/packages/R/r-bioc-biomformat/trunk/debian/changelog
trunk/packages/R/r-bioc-biomformat/trunk/debian/compat
trunk/packages/R/r-bioc-biomformat/trunk/debian/control
trunk/packages/R/r-bioc-biomformat/trunk/debian/copyright
trunk/packages/R/r-bioc-biomformat/trunk/debian/docs
trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/
trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/series
trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/use_debian_packaged_hdf5.patch
trunk/packages/R/r-bioc-biomformat/trunk/debian/rules
trunk/packages/R/r-bioc-biomformat/trunk/debian/source/
trunk/packages/R/r-bioc-biomformat/trunk/debian/source/format
trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/
trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/control
trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/run-unit-test
trunk/packages/R/r-bioc-biomformat/trunk/debian/watch
Log:
Really inject r-bioc-biomformat
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/README.test (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/README.test 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sh ./run-unit-test
+
+in order to confirm its integrity.
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/changelog (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/changelog 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,5 @@
+r-bioc-biomformat (1.0.2-1) UNRELEASED; urgency=low
+
+ * Initial release (closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Mon, 22 Aug 2016 22:15:51 +0200
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/compat
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/compat (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/compat 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1 @@
+9
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/control (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/control 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,35 @@
+Source: r-bioc-biomformat
+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-cran-plyr,
+ r-cran-jsonlite,
+ r-cran-matrix,
+ r-cran-hdf5
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-biomformat/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biomformat/trunk/
+Homepage: http://bioconductor.org/packages/release/bioc/html/biomformat.html
+
+Package: r-bioc-biomformat
+Architecture: all
+Depends: ${R:Depends},
+ ${misc:Depends},
+ r-cran-plyr,
+ r-cran-jsonlite,
+ r-cran-matrix,
+ r-cran-hdf5
+Description: GNU R interface package for the BIOM file format
+ This is an R package for interfacing with the BIOM format. This package
+ includes basic tools for reading biom-format files, accessing and
+ subsetting data tables from a biom object (which is more complex than a
+ single table), as well as limited support for writing a biom-object back
+ to a biom-format file. The design of this API is intended to match the
+ Python API and other tools included with the biom-format project, but
+ with a decidedly "R flavor" that should be familiar to R users. This
+ includes S4 classes and methods, as well as extensions of common core
+ functions/methods.
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/copyright (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/copyright 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: biomformat
+Upstream-Contact: Paul J. McMurdie <mcmurdie at stanford.edu>
+Source: http://www.bioconductor.org/packages/release/bioc/html/biomformat.html
+
+Files: *
+Copyright: 2012-2016 Paul J. McMurdie <mcmurdie at stanford.edu>
+License: GPL-2
+
+Files: debian/*
+Copyright: 2016 Andreas Tille <tille at debian.org>
+License: GPL-2
+
+License: GPL-2
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along
+ with this program; if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ .
+ You can find the text of GNU General Public License version 2.0
+ at /usr/share/common-licenses/GPL-2.
+
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/docs (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/docs 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,3 @@
+tests
+debian/README.test
+debian/tests/run-unit-test
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/series (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/series 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1 @@
+use_debian_packaged_hdf5.patch
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/use_debian_packaged_hdf5.patch
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/use_debian_packaged_hdf5.patch (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/patches/use_debian_packaged_hdf5.patch 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,23 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 22 Aug 2016 22:15:51 +0200
+Description: It seems there is no need to package BioConductor rhdf5 and we
+ wan go with r-cran-hdf5 - at least the test suite passes with this strategy
+
+--- a/DESCRIPTION
++++ b/DESCRIPTION
+@@ -13,7 +13,7 @@ Description: This is an R package for in
+ back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format
+ project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of
+ common core functions/methods.
+-Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2), rhdf5
++Imports: plyr (>= 1.8), jsonlite (>= 0.9.16), Matrix (>= 1.2)
+ Depends: R (>= 3.2), methods
+ Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6),
+ rmarkdown (>= 0.7)
+--- a/NAMESPACE
++++ b/NAMESPACE
+@@ -26,4 +26,3 @@ importFrom(plyr,d_ply)
+ importFrom(plyr,laply)
+ importFrom(plyr,ldply)
+ importFrom(plyr,llply)
+-importFrom(rhdf5,h5read)
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/rules (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/rules 2016-08-27 08:54:08 UTC (rev 22728)
@@ -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-biomformat/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/source/format
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/source/format (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/source/format 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/control (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/control 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-testthat
+Restrictions: allow-stderr
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/run-unit-test (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/tests/run-unit-test 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,13 @@
+#!/bin/sh -e
+
+oname=biomformat
+pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'`
+
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+ trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+LC_ALL=C R --no-save < testthat-biomformat.R
+rm -fr $ADTTMP/*
Added: trunk/packages/R/r-bioc-biomformat/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-biomformat/trunk/debian/watch (rev 0)
+++ trunk/packages/R/r-bioc-biomformat/trunk/debian/watch 2016-08-27 08:54:08 UTC (rev 22728)
@@ -0,0 +1,3 @@
+version=3
+opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \
+ http://www.bioconductor.org/packages/release/bioc/html/biomformat.html .*/biomformat_([\d\.]+)\.tar\.gz
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