[med-svn] [r-bioc-phyloseq] 02/11: Update packaging

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

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

commit 5c2bb7de00964e9655ab278a5c674bb64bea9d1a
Author: Andreas Tille <tille at debian.org>
Date:   Sat Aug 27 09:23:24 2016 +0000

    Update packaging
---
 debian/README.test         |  8 ++++++++
 debian/changelog           |  2 +-
 debian/control             | 18 ++++++++++++++----
 debian/docs                |  3 +++
 debian/tests/control       |  3 +++
 debian/tests/run-unit-test | 13 +++++++++++++
 6 files changed, 42 insertions(+), 5 deletions(-)

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
index 06a9db2..d96e971 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,6 @@
 r-bioc-phyloseq (1.16.2-1) UNRELEASED; urgency=low
 
   * Initial release (closes: #???)
-  TODO: https://bioconductor.org/packages/release/bioc/html/biomformat.html
+  TODO: r-bioc-biomformat #835579
 
  -- Andreas Tille <tille at debian.org>  Mon, 22 Aug 2016 22:15:51 +0200
diff --git a/debian/control b/debian/control
index 9ae37fc..f695292 100644
--- a/debian/control
+++ b/debian/control
@@ -8,6 +8,7 @@ Build-Depends: debhelper (>= 9),
                r-base-dev,
                r-bioc-biobase,
                r-bioc-biostrings,
+               r-bioc-biomformat,
                r-bioc-multtest,
                r-cran-ade4,
                r-cran-ape,
@@ -15,9 +16,7 @@ Build-Depends: debhelper (>= 9),
                r-cran-foreach,
                r-cran-ggplot2,
                r-cran-igraph,
-               r-cran-plyr,
-               r-cran-vegan,
-#            r-bioc-biomformat,
+               r-cran-vegan
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-phyloseq/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-phyloseq/trunk/
@@ -26,7 +25,18 @@ Homepage: http://bioconductor.org/packages/release/bioc/html/phyloseq.html
 Package: r-bioc-phyloseq
 Architecture: all
 Depends: ${R:Depends},
-         ${misc:Depends}
+         ${misc:Depends},
+         r-bioc-biobase,
+         r-bioc-biostrings,
+         r-bioc-biomformat,
+         r-bioc-multtest,
+         r-cran-ade4,
+         r-cran-ape,
+         r-cran-data.table,
+         r-cran-foreach,
+         r-cran-ggplot2,
+         r-cran-igraph,
+         r-cran-vegan
 Description: GNU R handling and analysis of high-throughput microbiome census data
  The Bioconductor module phyloseq provides a set of classes and tools to
  facilitate the import, storage, analysis, and graphical display of
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/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..b7ac9a9
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,13 @@
+#!/bin/sh -e
+
+oname=phyloseq
+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-phyloseq.R
+rm -fr $ADTTMP/*

-- 
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