[med-svn] [r-cran-adephylo] 03/11: Fix control and tests

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository r-cran-adephylo.

commit 94a30a40fc6d66fdbf92b26cd656aa1d1d023ade
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jun 29 11:21:18 2016 +0000

    Fix control and tests
---
 debian/README.test         |  7 +++----
 debian/changelog           |  1 -
 debian/control             | 10 +++++-----
 debian/docs                |  1 -
 debian/examples            |  1 +
 debian/tests/run-unit-test | 19 +++++++++++++------
 6 files changed, 22 insertions(+), 17 deletions(-)

diff --git a/debian/README.test b/debian/README.test
index 8d70ca3..55a9142 100644
--- a/debian/README.test
+++ b/debian/README.test
@@ -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.
diff --git a/debian/changelog b/debian/changelog
index 6d64689..9eefb4d 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -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
diff --git a/debian/control b/debian/control
index 09fb83d..aadfe34 100644
--- a/debian/control
+++ b/debian/control
@@ -5,12 +5,12 @@ Section: gnu-r
 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 @@ Package: r-cran-adephylo
 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.
diff --git a/debian/docs b/debian/docs
index 960011c..9a4f4f8 100644
--- a/debian/docs
+++ b/debian/docs
@@ -1,3 +1,2 @@
-tests
 debian/README.test
 debian/tests/run-unit-test
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..18244c8
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+vignettes
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index b1aa7d1..ced9b03 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -1,12 +1,19 @@
 #!/bin/sh -e
-
-oname=adegenet
-pkg=r-cran-`echo $oname | tr [A-Z] [a-z]`
+oname=adephylo
+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

-- 
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