[Debian-med-packaging] Bug#735547: autopkgtest fails on missing runit, stderr, and non-packaged "reactome.db" and "hom.Hs.inp.db"

[Martin Pitt]

Package: r-bioc-annotationdbi
Version: 1.24.0-1

Hello,

r-bioc-annotationdbi's autopkgtest currently fails [1]:

  Error in BiocGenerics:::testPackage("AnnotationDbi") : 
    RUnit package not found

After adding it (r-cran-runit), it fails because the test produces a
lot of stderror.

Attached debdiff fixes these, but the autopkgtest then fails with:

  Error in library("org.TguttataTestingSubset.eg.db") : 
    there is no package called 'org.TguttataTestingSubset.eg.db'
  Loading required package: hom.Hs.inp.db
  Error in eval(expr, envir, enclos) : object 'hom.Hs.inp.db' not found
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'hom.Hs.inp.db'
  Loading required package: reactome.db
  Error in eval(expr, envir, enclos) : object 'reactome.db' not found
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'reactome.db'

It seems these aren't packaged yet?

Thanks for considering,

Martin

[1] https://jenkins.qa.ubuntu.com/job/trusty-adt-r-bioc-annotationdbi/1/ARCH=i386,label=adt/console
-- 
Martin Pitt                        | http://www.piware.de
Ubuntu Developer (www.ubuntu.com)  | Debian Developer  (www.debian.org)
-------------- next part --------------
diff -Nru r-bioc-annotationdbi-1.24.0/debian/changelog r-bioc-annotationdbi-1.24.0/debian/changelog
--- r-bioc-annotationdbi-1.24.0/debian/changelog	2013-12-28 16:31:26.000000000 +0100
+++ r-bioc-annotationdbi-1.24.0/debian/changelog	2014-01-16 12:25:12.000000000 +0100
@@ -1,3 +1,10 @@
+r-bioc-annotationdbi (1.24.0-1ubuntu1) UNRELEASED; urgency=medium
+
+  * debian/tests/control: Add missing r-cran-runit test dependency, and allow
+    stderr output.
+
+ -- Martin Pitt <martin.pitt at ubuntu.com>  Thu, 16 Jan 2014 12:24:53 +0100
+
 r-bioc-annotationdbi (1.24.0-1) unstable; urgency=medium
 
   * New upstream version
diff -Nru r-bioc-annotationdbi-1.24.0/debian/tests/control r-bioc-annotationdbi-1.24.0/debian/tests/control
--- r-bioc-annotationdbi-1.24.0/debian/tests/control	2013-11-05 09:42:06.000000000 +0100
+++ r-bioc-annotationdbi-1.24.0/debian/tests/control	2014-01-16 12:24:51.000000000 +0100
@@ -1 +1,3 @@
 Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr
-------------- next part --------------
A non-text attachment was scrubbed...
Name: signature.asc
Type: application/pgp-signature
Size: 836 bytes
Desc: Digital signature
URL: <http://lists.alioth.debian.org/pipermail/debian-med-packaging/attachments/20140116/ecffb6d4/attachment.sig>