[med-svn] r18352 - in trunk/packages/R/r-bioc-makecdfenv/trunk/debian: . tests
Andreas Tille
tille at moszumanska.debian.org
Mon Oct 20 06:31:45 UTC 2014
Author: tille
Date: 2014-10-20 06:31:45 +0000 (Mon, 20 Oct 2014)
New Revision: 18352
Added:
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/examples
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/control
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/run-unit-test
Modified:
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/README.test
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/changelog
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/control
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/copyright
trunk/packages/R/r-bioc-makecdfenv/trunk/debian/docs
Log:
New upstream version, added autopkgtest
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/README.test 2014-10-20 06:14:14 UTC (rev 18351)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/README.test 2014-10-20 06:31:45 UTC (rev 18352)
@@ -1,5 +1,8 @@
Notes on how this package can be tested.
────────────────────────────────────────
-This package can be tested by loading it into R with the command
-‘library(makecdfenv)’ in order to confirm its integrity.
+To run the unit tests provided by the package you can do
+
+ sh run-unit-test
+
+in this directory.
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/changelog 2014-10-20 06:14:14 UTC (rev 18351)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/changelog 2014-10-20 06:31:45 UTC (rev 18352)
@@ -1,3 +1,11 @@
+r-bioc-makecdfenv (1.42.0-1) experimental; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * Add autopkgtest
+
+ -- Andreas Tille <tille at debian.org> Mon, 20 Oct 2014 07:29:43 +0200
+
r-bioc-makecdfenv (1.40.0-1) unstable; urgency=medium
* New upstream version
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/control 2014-10-20 06:14:14 UTC (rev 18351)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/control 2014-10-20 06:31:45 UTC (rev 18352)
@@ -6,10 +6,8 @@
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
- r-bioc-biobase,
- r-bioc-affyio,
- r-bioc-affy
-Standards-Version: 3.9.5
+ r-bioc-affy (>= 1.44.0)
+Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-makecdfenv/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-makecdfenv/trunk/
Homepage: http://bioconductor.org/packages/release/bioc/html/makecdfenv.html
@@ -19,9 +17,7 @@
Depends: ${R:Depends},
${misc:Depends},
${shlibs:Depends},
- r-bioc-biobase,
- r-bioc-affyio,
- r-bioc-affy
+ r-bioc-affy (>= 1.44.0)
Description: BioConductor CDF Environment Maker
This package has two functions. One reads a Affymetrix chip description
file (CDF) and creates a hash table environment containing the
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/copyright 2014-10-20 06:14:14 UTC (rev 18351)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/copyright 2014-10-20 06:31:45 UTC (rev 18352)
@@ -4,7 +4,7 @@
Source: http://www.bioconductor.org/packages/release/bioc/html/makecdfenv.html
Files: *
-Copyright: © 2006-2013 Rafael A. Irizarry <rafa at jhu.edu>,
+Copyright: © 2006-2014 Rafael A. Irizarry <rafa at jhu.edu>,
Laurent Gautier <laurent at cbs.dtu.dk>,
Wolfgang Huber <w.huber at dkfz-heidelberg.de>,
Ben Bolstad <bmb at bmbolstad.com>
@@ -12,7 +12,7 @@
Files: debian/*
-Copyright: 2013 Andreas Tille <tille at debian.org>
+Copyright: 2013-2014 Andreas Tille <tille at debian.org>
License: Artistic-2.0
License: Artistic-2.0
Modified: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/docs 2014-10-20 06:14:14 UTC (rev 18351)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/docs 2014-10-20 06:31:45 UTC (rev 18352)
@@ -1 +1,2 @@
debian/README.test
+debian/tests/run-unit-test
Added: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/examples
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/examples (rev 0)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/examples 2014-10-20 06:31:45 UTC (rev 18352)
@@ -0,0 +1 @@
+vignettes
Added: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/control (rev 0)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/control 2014-10-20 06:31:45 UTC (rev 18352)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
Added: trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/run-unit-test (rev 0)
+++ trunk/packages/R/r-bioc-makecdfenv/trunk/debian/tests/run-unit-test 2014-10-20 06:31:45 UTC (rev 18352)
@@ -0,0 +1,18 @@
+#!/bin/sh -e
+oname=makecdfenv
+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 \{\} \;
+for rnw in `ls *.[rRS]nw` ; do
+rfile=`echo $rnw | sed 's/\.[rRS]nw/.R/'`
+R --no-save <<EOT
+ Stangle("$rnw")
+ source("$rfile", echo=TRUE)
+EOT
+done
+rm -rf *
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