[med-svn] r19186 - in trunk/packages/R/r-bioc-snpstats/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2015-05-09 21:17:21 +0000 (Sat, 09 May 2015)
New Revision: 19186

Modified:
   trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog
   trunk/packages/R/r-bioc-snpstats/trunk/debian/control
   trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test
   trunk/packages/R/r-bioc-snpstats/trunk/debian/watch
Log:
Exclude tests needing not packaged CRAN packages


Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog	2015-05-09 21:09:19 UTC (rev 19185)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog	2015-05-09 21:17:21 UTC (rev 19186)
@@ -1,7 +1,8 @@
 r-bioc-snpstats (1.18.0+dfsg-1) unstable; urgency=medium
 
   * New upstream version
-    TODO: Testsuite uses http://cran.r-project.org/web/packages/hexbin/
+  * Exclude tests needing not packaged CRAN packages
+  * d/watch: proper versionmangling
 
  -- Andreas Tille <tille at debian.org>  Sat, 09 May 2015 08:31:15 +0200
 

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/control	2015-05-09 21:09:19 UTC (rev 19185)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/control	2015-05-09 21:17:21 UTC (rev 19186)
@@ -24,6 +24,7 @@
          r-cran-survival,
          r-cran-matrix,
          r-bioc-biocgenerics (>= 0.12.0)
+Suggests: r-cran-hexbin
 Description: BioConductor SnpMatrix and XSnpMatrix classes and methods
  This BioConductor package provides R functions to work with
  SnpMatrix and XSnpMatrix classes and methods.

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test	2015-05-09 21:09:19 UTC (rev 19185)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test	2015-05-09 21:17:21 UTC (rev 19186)
@@ -8,12 +8,22 @@
 fi
 cd $ADTTMP
 cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
-gunzip *.gz
+find . -name "*.gz" -exec gunzip \{\} \;
+export LC_ALL=C
 for rnw in *.Rnw ; do
-rfile=`basename $rnw nw`
-R --no-save <<EOT
-  Stangle("$rnw")
-  source("$rfile", echo=TRUE)
+    echo "====================== $rnw ============================"
+    rfile=`basename $rnw nw`
+    if [ "$rnw" = "imputation-vignette.Rnw" ] ; then # -o "$rnw" = "ld-vignette.Rnw" ]
+        echo "Test "$rnw" needs r-cran-hexbin which is not yet packaged."
+    else
+        if [ "$rnw" = "snpStats-vignette.Rnw" ] ; then
+            echo "Test $rnw needs allest[""rs10882596""] but it is not clear where to get this."
+        else
+            R --no-save <<EOT
+                Stangle("$rnw")
+                source("$rfile", echo=TRUE)
 EOT
+        fi
+    fi
 done
 

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/watch	2015-05-09 21:09:19 UTC (rev 19185)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/watch	2015-05-09 21:17:21 UTC (rev 19186)
@@ -1,3 +1,3 @@
 version=3
-opts=uversionmangle=s/$/+dfsg/,downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,downloadurlmangle=s/\.\./packages\/release\/bioc/" \
  http://www.bioconductor.org/packages/release/bioc/html/snpStats.html .*/snpStats_([\d\.]+)\.tar\.gz