[med-svn] [r-cran-metamix] 02/02: Commit initial debian/ dir
Andreas Tille
tille at debian.org
Mon Aug 17 10:32:25 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-cran-metamix.
commit 4dfe8b3be40bff6e5cd6bdb7b8b172e6708720a4
Author: Andreas Tille <tille at debian.org>
Date: Mon Aug 17 12:27:02 2015 +0200
Commit initial debian/ dir
---
debian/README.test | 14 ++++++++++++++
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 25 +++++++++++++++++++++++++
debian/copyright | 29 +++++++++++++++++++++++++++++
debian/rules | 3 +++
debian/source/format | 1 +
debian/source/include-binaries | 1 +
debian/tests/control | 3 +++
debian/tests/run-unit-test | 23 +++++++++++++++++++++++
debian/upstream/metadata | 34 ++++++++++++++++++++++++++++++++++
debian/watch | 3 +++
12 files changed, 142 insertions(+)
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..ccabf7e
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,14 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests provided by the package you can do
+
+ sh run-unit-test
+
+in this directory.
+
+Please note: It seems that the control output does not seem to correspond
+to the testing code. So there is some resulting difference that needs to
+be sorted out with upstream.
+
+ -- Andreas Tille <tille at debian.org> Fri, 27 Jun 2014 19:02:17 +0200
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..cc57d07
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+r-cran-metamix (0.2-1) UNRELEASED; urgency=medium
+
+ * Initial upload (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org> Mon, 17 Aug 2015 11:42:25 +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..2f6de93
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,25 @@
+Source: r-cran-metamix
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Alba Crespi <crespialba+debian at gmail.com>
+Section: gnu-r
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ cdbs,
+ r-base-dev
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/r-cran-metamix.git
+Vcs-Git: git://anonscm.debian.org/debian-med/r-cran-metamix.git
+Homepage: https://cran.r-project.org/web/packages/metaMix/index.html
+
+Package: r-cran-metamix
+Architecture: any
+Depends: ${R:Depends},
+ ${misc:Depends},
+ ${shlibs:Depends}
+Description: GNU R bayesian mixture analysis for metagenomic community profiling
+ Resolves complex metagenomic mixtures by analysing deep sequencing
+ data, using a mixture model based approach. The use of parallel Monte
+ Carlo Markov chains for the exploration of the species space enables
+ the identification of the set of species more likely to contribute to
+ the mixture.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..798beb8
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Names: metaMix
+Upstream-Contact: Sofia Morfopoulou <sofia.morfopoulou.10 at ucl.ac.uk>
+Source: https://cran.r-project.org/web/packages/metaMix/index.html
+
+Files: *
+Copyright: 2014-2015 Sofia Morfopoulou <sofia.morfopoulou.10 at ucl.ac.uk>
+License: GPL-3
+
+Files: debian/*
+Copyright: 2015 Andreas Tille <tille at debian.org>
+License: GPL-3
+
+License: GPL-3
+ 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 3 of the License.
+ .
+ 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.
+Comment: On Debian systems, a copy of the GNU General Public version 3
+ is available in ‘/usr/share/common-licenses/GPL-3’.
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..2fbba2d
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,3 @@
+#!/usr/bin/make -f
+
+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/source/include-binaries b/debian/source/include-binaries
new file mode 100644
index 0000000..ba65153
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1 @@
+debian/patches/fix-unit-test-result.patch
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..5f35a24
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,23 @@
+#!/bin/sh -e
+
+pkg=r-bioc-edger
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+gunzip *.gz
+export LC_ALL=C
+for test in *R
+do
+ R CMD BATCH ${test}
+ R CMD Rdiff ${test}out.save* ${test}out
+ if [ ! $? ] ; then
+ echo "Test ${test} failed"
+ exit 1
+ else
+ echo "Test ${test} passed"
+ fi
+ rm -f ${test}out .RData
+done
+rm -f $ADTTMP/*
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..38a6d97
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,34 @@
+Archive: Bioconductor
+Bioconductor: edgeR
+Contact: Mark Robinson <mrobinson at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>
+Download: http://bioconductor.org/packages/release/bioc/src/contrib/
+Homepage: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
+Name: edgeR
+Reference:
+ - author: Mark D. Robinson and Davis J. McCarthy and Gordon K. Smyth
+ title: "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data"
+ journal: Bioinformatics
+ volume: 26,
+ pages: 139-140
+ year: 2010
+ DOI: 10.1093/bioinformatics/btp616
+ PMID: 19910308
+ URL: http://bioinformatics.oxfordjournals.org/content/26/1/139
+ eprint: http://bioinformatics.oxfordjournals.org/content/26/1/139.full.pdf+html
+ - author: Mark D. Robinson and Gordon K. Smyth
+ title: Moderated statistical tests for assessing differences in tag abundance
+ journal: Bioinformatics
+ volume: 23
+ number: 21
+ pages: 2881-2887
+ doi: 10.1093/bioinformatics/btm453
+ PMID: 17881408
+ year: 2007
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2881
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2881.pdf
+Watch: |
+ version=3
+
+ # This tracks the current stable version of edgeR
+ opts="dversionmangle=s|~dfsg||,downloadurlmangle=s|\.\.|packages/release/bioc|" \
+ http://www.bioconductor.org/packages/release/bioc/html/edgeR.html .*/edgeR_(.*).tar.gz
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..33ddbc0
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+
+https://cran.r-project.org/src/contrib/metaMix_(\d[\d.]*)\.tar\.gz
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