[med-svn] r22256 - in trunk/packages/R/r-cran-adephylo/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2016-06-29 11:21:18 +0000 (Wed, 29 Jun 2016)
New Revision: 22256

Added:
   trunk/packages/R/r-cran-adephylo/trunk/debian/examples
Modified:
   trunk/packages/R/r-cran-adephylo/trunk/debian/README.test
   trunk/packages/R/r-cran-adephylo/trunk/debian/changelog
   trunk/packages/R/r-cran-adephylo/trunk/debian/control
   trunk/packages/R/r-cran-adephylo/trunk/debian/docs
   trunk/packages/R/r-cran-adephylo/trunk/debian/tests/run-unit-test
Log:
Fix control and tests


Modified: trunk/packages/R/r-cran-adephylo/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-cran-adephylo/trunk/debian/README.test	2016-06-29 10:18:49 UTC (rev 22255)
+++ trunk/packages/R/r-cran-adephylo/trunk/debian/README.test	2016-06-29 11:21:18 UTC (rev 22256)
@@ -1,9 +1,8 @@
 Notes on how this package can be tested.
 ────────────────────────────────────────
 
-This package can be tested by running the provided test:
+To run the unit tests provided by the package you can do
 
-cd tests
-LC_ALL=C R --no-save < testthat.R
+   sh  run-unit-test
 
-in order to confirm its integrity.
+in this directory.

Modified: trunk/packages/R/r-cran-adephylo/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-cran-adephylo/trunk/debian/changelog	2016-06-29 10:18:49 UTC (rev 22255)
+++ trunk/packages/R/r-cran-adephylo/trunk/debian/changelog	2016-06-29 11:21:18 UTC (rev 22256)
@@ -1,6 +1,5 @@
 r-cran-adephylo (1.1-6-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #???)
-  TODO: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-adegenet/trunk/
 
  -- Andreas Tille <tille at debian.org>  Tue, 22 Mar 2016 21:32:09 +0100

Modified: trunk/packages/R/r-cran-adephylo/trunk/debian/control
===================================================================
--- trunk/packages/R/r-cran-adephylo/trunk/debian/control	2016-06-29 10:18:49 UTC (rev 22255)
+++ trunk/packages/R/r-cran-adephylo/trunk/debian/control	2016-06-29 11:21:18 UTC (rev 22256)
@@ -5,12 +5,12 @@
 Priority: optional
 Build-Depends: debhelper (>= 9),
                cdbs,
-               r-base-dev
+               r-base-dev,
                r-cran-ade4,
                r-cran-ape,
                r-cran-phylobase,
-# r-cran-adegenet
-Standards-Version: 3.9.7
+               r-cran-adegenet
+Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-adephylo/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-adephylo/trunk/
 Homepage: https://cran.r-project.org/web/packages/adephylo/
@@ -19,11 +19,11 @@
 Architecture: any
 Depends: ${misc:Depends},
          ${shlibs:Depends},
-         ${R:Depends}
+         ${R:Depends},
          r-cran-ade4,
          r-cran-ape,
          r-cran-phylobase,
-# r-cran-adegenet
+         r-cran-adegenet
 Description: GNU R exploratory analyses for the phylogenetic comparative method
  This GNU R package provides multivariate tools to analyze comparative
  data, i.e. a phylogeny and some traits measured for each taxa.

Modified: trunk/packages/R/r-cran-adephylo/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-cran-adephylo/trunk/debian/docs	2016-06-29 10:18:49 UTC (rev 22255)
+++ trunk/packages/R/r-cran-adephylo/trunk/debian/docs	2016-06-29 11:21:18 UTC (rev 22256)
@@ -1,3 +1,2 @@
-tests
 debian/README.test
 debian/tests/run-unit-test

Added: trunk/packages/R/r-cran-adephylo/trunk/debian/examples
===================================================================
--- trunk/packages/R/r-cran-adephylo/trunk/debian/examples	                        (rev 0)
+++ trunk/packages/R/r-cran-adephylo/trunk/debian/examples	2016-06-29 11:21:18 UTC (rev 22256)
@@ -0,0 +1 @@
+vignettes

Modified: trunk/packages/R/r-cran-adephylo/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-cran-adephylo/trunk/debian/tests/run-unit-test	2016-06-29 10:18:49 UTC (rev 22255)
+++ trunk/packages/R/r-cran-adephylo/trunk/debian/tests/run-unit-test	2016-06-29 11:21:18 UTC (rev 22256)
@@ -1,12 +1,19 @@
 #!/bin/sh -e
+oname=adephylo
+pkg=r-cran-`echo $oname | tr '[A-Z]' '[a-z]'`
 
-oname=adegenet
-pkg=r-cran-`echo $oname | tr [A-Z] [a-z]`
-
 if [ "$ADTTMP" = "" ] ; then
   ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
 fi
 cd $ADTTMP
-cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
-LC_ALL=C R --no-save < testthat.R
-rm -fr $ADTTMP/*
+cp /usr/share/doc/$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("$rfile", echo=TRUE)
+EOT
+  echo "$rnw passed"
+done