[med-svn] [r-bioc-ebseq] 04/06: Add autopkgtest

[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-ebseq.

commit ae20873097056b874ce9490494e53a0598f5dc23
Author: Andreas Tille <tille at debian.org>
Date:   Sun Nov 8 21:26:54 2015 +0100

    Add autopkgtest
---
 debian/README.test         |  8 ++++++++
 debian/control             |  7 +++++--
 debian/docs                |  2 ++
 debian/examples            |  1 +
 debian/tests/control       |  5 +++++
 debian/tests/run-unit-test | 19 +++++++++++++++++++
 6 files changed, 40 insertions(+), 2 deletions(-)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..55a9142
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+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.
diff --git a/debian/control b/debian/control
index d87c723..b6e1a4a 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,8 @@ Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,
                r-cran-gplots,
-               r-cran-blockmodeling
+               r-cran-blockmodeling,
+               r-cran-testthat
 Standards-Version: 3.9.6
 Homepage: https://www.biostat.wisc.edu/~kendzior/EBSEQ/
 
@@ -15,7 +16,9 @@ Package: r-bioc-ebseq
 Architecture: all
 Depends: ${R:Depends},
          ${misc:Depends},
-         r-cran-gplots
+         r-cran-gplots,
+         r-cran-blockmodeling,
+         r-cran-testthat
 Description: R package for RNA-Seq Differential Expression Analysis
  r-bioc-ebseq is an R package for identifying genes and isoforms differentially
  expressed (DE) across two or more biological conditions in an RNA-seq
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..9a4f4f8
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..18244c8
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+vignettes
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..3edd424
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,5 @@
+Tests: run-unit-test
+# The following dependencies are not available so this autopkgtest is disabled
+Depends: @
+###, r-bioc-biocstyle, r-bioc-bsgenome.hsapiens.ucsc.hg19
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..d134fec
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,19 @@
+#!/bin/sh -e
+oname=ebseq
+pkg=r-bioc-`echo $oname | tr [A-Z] [a-z]`
+
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
+find . -name "*.gz" -exec gunzip \{\} \;
+export LC_ALL=C
+for rnw in `ls *.[rR]nw` ; do
+rfile=`echo $rnw | sed 's/\.[rR]nw/.R/'`
+R --no-save <<EOT
+  Stangle("$rnw")
+  source("$rfile", echo=TRUE)
+EOT
+done
+# rm -rf *

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