[med-svn] r17649 - in trunk/packages/R/r-bioc-gviz/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2014-08-08 13:01:07 +0000 (Fri, 08 Aug 2014)
New Revision: 17649

Added:
   trunk/packages/R/r-bioc-gviz/trunk/debian/tests/
   trunk/packages/R/r-bioc-gviz/trunk/debian/tests/control_unused
   trunk/packages/R/r-bioc-gviz/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-gviz/trunk/debian/README.test
   trunk/packages/R/r-bioc-gviz/trunk/debian/changelog
Log:
New upstream source and add better / more precise advise how the package can be tested.  No autopkgtest since it requires 800MB data package


Modified: trunk/packages/R/r-bioc-gviz/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/README.test	2014-08-08 12:55:25 UTC (rev 17648)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/README.test	2014-08-08 13:01:07 UTC (rev 17649)
@@ -1,5 +1,24 @@
 Notes on how this package can be tested.
 ────────────────────────────────────────
 
-This package can be tested by loading it into R with the command
-‘library(Gviz)’ in order to confirm its integrity.
+This package can be tested be rerunning the vignettes.  However
+you need to install the following stuff from BioConductto first:
+
+   http://bioconductor.org/packages/release/bioc/html/BiocStyle.html
+   http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html
+
+To simplify the installation of the large data package you can use the Debian
+packaging which is prepared at
+
+   svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-bsgenome.hsapiens.ucsc.hg19/trunk/
+
+and create a Debian packagage.  Currently there is no preparation done
+for a r-bioc-biocstyle package - may be this can be changed at request.
+Once you installed this data you can run script which is provided in
+the package source as
+
+    debian/tests/run-unit-test
+
+to confirm the integrity of the package.
+
+ -- Andreas Tille <tille at debian.org>  Fri, 08 Aug 2014 13:37:40 +0200

Modified: trunk/packages/R/r-bioc-gviz/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/changelog	2014-08-08 12:55:25 UTC (rev 17648)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/changelog	2014-08-08 13:01:07 UTC (rev 17649)
@@ -1,3 +1,10 @@
+r-bioc-gviz (1.8.4-1) unstable; urgency=medium
+
+  * New upstream version
+  * Add better advise how the package can be tested
+
+ -- Andreas Tille <tille at debian.org>  Fri, 08 Aug 2014 14:18:07 +0200
+
 r-bioc-gviz (1.8.3-1) unstable; urgency=medium
 
   * New upstream version

Added: trunk/packages/R/r-bioc-gviz/trunk/debian/tests/control_unused
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/tests/control_unused	                        (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/tests/control_unused	2014-08-08 13:01:07 UTC (rev 17649)
@@ -0,0 +1,4 @@
+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

Added: trunk/packages/R/r-bioc-gviz/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-gviz/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-gviz/trunk/debian/tests/run-unit-test	2014-08-08 13:01:07 UTC (rev 17649)
@@ -0,0 +1,18 @@
+#!/bin/sh -e
+oname=Gviz
+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
+gunzip *.gz
+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 *