[med-svn] r22729 - in trunk/packages/R/r-bioc-phyloseq/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2016-08-27 09:23:24 +0000 (Sat, 27 Aug 2016)
New Revision: 22729

Added:
   trunk/packages/R/r-bioc-phyloseq/trunk/debian/README.test
   trunk/packages/R/r-bioc-phyloseq/trunk/debian/docs
   trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/
   trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/control
   trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-phyloseq/trunk/debian/changelog
   trunk/packages/R/r-bioc-phyloseq/trunk/debian/control
Log:
Update packaging


Added: trunk/packages/R/r-bioc-phyloseq/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-phyloseq/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/R/r-bioc-phyloseq/trunk/debian/README.test	2016-08-27 09:23:24 UTC (rev 22729)
@@ -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.

Modified: trunk/packages/R/r-bioc-phyloseq/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-phyloseq/trunk/debian/changelog	2016-08-27 08:54:08 UTC (rev 22728)
+++ trunk/packages/R/r-bioc-phyloseq/trunk/debian/changelog	2016-08-27 09:23:24 UTC (rev 22729)
@@ -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

Modified: trunk/packages/R/r-bioc-phyloseq/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-phyloseq/trunk/debian/control	2016-08-27 08:54:08 UTC (rev 22728)
+++ trunk/packages/R/r-bioc-phyloseq/trunk/debian/control	2016-08-27 09:23:24 UTC (rev 22729)
@@ -8,6 +8,7 @@
                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 @@
                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 @@
 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

Added: trunk/packages/R/r-bioc-phyloseq/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-phyloseq/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/R/r-bioc-phyloseq/trunk/debian/docs	2016-08-27 09:23:24 UTC (rev 22729)
@@ -0,0 +1,3 @@
+tests
+debian/README.test
+debian/tests/run-unit-test

Added: trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/control	2016-08-27 09:23:24 UTC (rev 22729)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-testthat
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-phyloseq/trunk/debian/tests/run-unit-test	2016-08-27 09:23:24 UTC (rev 22729)
@@ -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/*