[med-svn] [r-bioc-biomformat] 02/08: Really inject r-bioc-biomformat
Andreas Tille
tille at debian.org
Sun Sep 24 07:03:36 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-biomformat.
commit 16da9b32ea857eef16ab22c6a0b9f40a30d8e218
Author: Andreas Tille <tille at debian.org>
Date: Sat Aug 27 08:54:08 2016 +0000
Really inject r-bioc-biomformat
---
debian/README.test | 8 ++++++
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 35 +++++++++++++++++++++++++++
debian/copyright | 31 ++++++++++++++++++++++++
debian/docs | 3 +++
debian/patches/series | 1 +
debian/patches/use_debian_packaged_hdf5.patch | 23 ++++++++++++++++++
debian/rules | 4 +++
debian/source/format | 1 +
debian/tests/control | 3 +++
debian/tests/run-unit-test | 13 ++++++++++
debian/watch | 3 +++
13 files changed, 131 insertions(+)
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..53fb4d7
--- /dev/null
+++ b/debian/README.test
@@ -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.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..b0de1fa
--- /dev/null
+++ b/debian/changelog
@@ -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
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..b0e8237
--- /dev/null
+++ b/debian/control
@@ -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.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..5001e28
--- /dev/null
+++ b/debian/copyright
@@ -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.
+
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..960011c
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+tests
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..f8768ac
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_debian_packaged_hdf5.patch
diff --git a/debian/patches/use_debian_packaged_hdf5.patch b/debian/patches/use_debian_packaged_hdf5.patch
new file mode 100644
index 0000000..fb75d25
--- /dev/null
+++ b/debian/patches/use_debian_packaged_hdf5.patch
@@ -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)
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/tests/control b/debian/tests/control
new file mode 100644
index 0000000..b044b0c
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-testthat
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..f89e590
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -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/*
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..232d2d5
--- /dev/null
+++ b/debian/watch
@@ -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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