[med-svn] r21779 - in trunk/packages/R/r-bioc-aroma.light/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2016-04-28 08:51:38 +0000 (Thu, 28 Apr 2016)
New Revision: 21779

Modified:
   trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog
   trunk/packages/R/r-bioc-aroma.light/trunk/debian/control
   trunk/packages/R/r-bioc-aroma.light/trunk/debian/tests/run-unit-test
Log:
Autopkgtest would need r-cran-princurve.  Add this not yet packaged R package to Suggests and remove those parts from the test suite that are depending from it



Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog	2016-04-28 07:34:21 UTC (rev 21778)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/changelog	2016-04-28 08:51:38 UTC (rev 21779)
@@ -1,3 +1,11 @@
+r-bioc-aroma.light (3.0.0-2) UNRELEASED; urgency=medium
+
+  * Autopkgtest would need r-cran-princurve.  Add this not yet packaged
+    R package to Suggests and remove those parts from the test suite that
+    are depending from it
+
+ -- Andreas Tille <tille at debian.org>  Thu, 28 Apr 2016 10:49:04 +0200
+
 r-bioc-aroma.light (3.0.0-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/control	2016-04-28 07:34:21 UTC (rev 21778)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/control	2016-04-28 08:51:38 UTC (rev 21779)
@@ -21,6 +21,7 @@
          r-cran-r.methodss3,
          r-cran-matrixstats (>= 0.14.0),
          r-cran-r.utils
+Suggests: r-cran-princurve
 Description: BioConductor methods normalization and visualization of microarray data
  This BioConductor module provides light-weight methods for
  normalization and visualization of microarray data using only basic R

Modified: trunk/packages/R/r-bioc-aroma.light/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-aroma.light/trunk/debian/tests/run-unit-test	2016-04-28 07:34:21 UTC (rev 21778)
+++ trunk/packages/R/r-bioc-aroma.light/trunk/debian/tests/run-unit-test	2016-04-28 08:51:38 UTC (rev 21779)
@@ -1,6 +1,7 @@
 #!/bin/sh -e
+
 oname=aroma.light
-pkg=r-bioc-`echo $oname | tr [A-Z] [a-z]`
+pkg=r-bioc-`echo $oname | tr '[A-Z]' '[a-z]'`
 
 if [ "$ADTTMP" = "" ] ; then
   ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
@@ -9,6 +10,12 @@
 cp /usr/share/doc/$pkg/tests/* $ADTTMP
 find . -name "*.gz" -exec gunzip \{\} \;
 for runtest in `ls *.R` ; do
+   if grep -q fitPrincipalCurve $runtest ; then
+      # Full test would beed princurve which is not packaged yet
+      # Just remove the code after this function was used from the test
+      echo '*** strip test since r-cran-princurve is not available as Debian package ***'
+      sed -i '/fitPrincipalCurve/,$d' $runtest
+   fi
    LC_ALL=C R --no-save < $runtest >/dev/null
    if [ ! $? ] ; then
      echo "Test ${runtest} failed"