[med-svn] [r-bioc-geneplotter] 04/11: Do not run autopkgtest which requires large database packages. Add a hint in README.test instead how users might be able to test after installing the databases manually

[Andreas Tille]

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

tille pushed a commit to branch master
in repository r-bioc-geneplotter.

commit 002ad7ce249e248692dc2e25b88ba8d549d5aceb
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jan 15 15:28:50 2017 +0100

    Do not run autopkgtest which requires large database packages.  Add a hint in README.test instead how users might be able to test after installing the databases manually
---
 debian/README.test                           |  4 +++-
 debian/changelog                             | 11 ++++++-----
 debian/tests/{control => control_do_not_run} |  0
 debian/tests/run-unit-test                   | 10 +---------
 4 files changed, 10 insertions(+), 15 deletions(-)

diff --git a/debian/README.test b/debian/README.test
index 55a9142..4d72eb3 100644
--- a/debian/README.test
+++ b/debian/README.test
@@ -1,7 +1,9 @@
 Notes on how this package can be tested.
 ────────────────────────────────────────
 
-To run the unit tests provided by the package you can do
+To run the unit tests provided by the package you need to install the two
+BioConductor database packages hu6800.db and hgu95av2.db manually since
+these are not packaged for Debian.  Once this is done you can do
 
    sh  run-unit-test
 
diff --git a/debian/changelog b/debian/changelog
index aa8621a..f7927fb 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,12 +1,13 @@
-r-bioc-geneplotter (1.52.0-2) UNRELEASED; urgency=medium
+r-bioc-geneplotter (1.52.0-2) unstable; urgency=medium
 
-  * Try crude hacks to strip unpackaged databases from vignettes to
-    safe the idea doing autopkgtests.  May be its not worth the hassle
-    and test should be dropped at all but at least now it works.
+  * Team upload
+  * Do not run autopkgtest which requires large database packages.  Add a
+    hint in README.test instead how users might be able to test after
+    installing the databases manually
   * debhelper 10
   * d/watch: version=4
 
- -- Andreas Tille <tille at debian.org>  Sun, 15 Jan 2017 15:16:12 +0100
+ -- Andreas Tille <tille at debian.org>  Sun, 15 Jan 2017 15:18:47 +0100
 
 r-bioc-geneplotter (1.52.0-1) unstable; urgency=medium
 
diff --git a/debian/tests/control b/debian/tests/control_do_not_run
similarity index 100%
rename from debian/tests/control
rename to debian/tests/control_do_not_run
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index b653388..7aa573d 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -4,21 +4,13 @@ pkg=r-bioc-`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
+  trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
 fi
 cd $ADTTMP
 cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
 find . -name "*.gz" -exec gunzip \{\} \;
-set -x
 for rnw in `ls *.[rRS]nw` ; do
 rfile=`echo $rnw | sed 's/\.[rRS]nw/.R/'`
-# Database hu6800.db is not packaged so do not load it inside the test
-# Dealing with hgu95av2.db is even harder - its needed in the end of visualize.Rnw
-# FIXME: May be this test should be skipped at all since its not maintainable
-sed -i -e '/library("hu6800.db")/d' \
-       -e 's/\(VignetteDepends{Biobase, annotate, geneplotter\), hgu95av2.db/\1/' \
-       -e '95,152d' \
-   $rnw
 R --no-save <<EOT
   Stangle("$rnw")
   source("$rfile", echo=TRUE)

-- 
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