[med-svn] r17435 - trunk/packages/R/r-bioc-rsamtools/trunk/debian

[Andreas Tille]

Author: tille
Date: 2014-07-09 12:56:21 +0000 (Wed, 09 Jul 2014)
New Revision: 17435

Modified:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
Log:
Sort out issues around test suite and close bug which should have been closed even in previous upload


Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test	2014-07-09 11:52:50 UTC (rev 17434)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/README.test	2014-07-09 12:56:21 UTC (rev 17435)
@@ -1,27 +1,15 @@
 Notes on how this package can be tested.
 ────────────────────────────────────────
 
-This package contains a test suite which depends from a dataset provided at
+Please make sure you have installed the Recommended package
+r-bioc-shortread.  Then you should be able to successfully run the test
+suite by doing
 
-  http://bioconductor.org/packages/release/data/experiment/html/pasillaBamSubset.html
-
-You can also create a Debian package from this data.  The packaging code is
-available in the Debian Med repository at
-
-  svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-pasillabamsubset/trunk/
-
-Once you have installed this please also make sure you have installed the
-Suggested package r-bioc-shortread.  Then you should be able to successfully
-run the test suite by doing
-
 R --no-save <<EOT
 BiocGenerics:::testPackage('Rsamtools')
 EOT
 
-Any problems with this test suite should be reportet via
+Currently one our of 73 tests is failing which is sorted out with
+upstream before an autopkgtest will be provided.
 
-   reportbug r-bioc-rsamtools
-
-to the Debian bug tracking system.
-
  -- Andreas Tille <tille at debian.org>  Mon, 16 Jun 2014 16:28:55 +0200

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2014-07-09 11:52:50 UTC (rev 17434)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2014-07-09 12:56:21 UTC (rev 17435)
@@ -1,6 +1,9 @@
-r-bioc-rsamtools (1.16.1-2) UNRELEASED; urgency=medium
+r-bioc-rsamtools (1.16.1-2) unstable; urgency=medium
 
   * debian/README.test: Fix advise for testing the package
+  * debian/control: Recommends: r-bioc-shortread
+  * Rebuild against recent BioC tools
+    Closes: #753233
 
  -- Andreas Tille <tille at debian.org>  Wed, 09 Jul 2014 13:38:19 +0200
 

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2014-07-09 11:52:50 UTC (rev 17434)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2014-07-09 12:56:21 UTC (rev 17435)
@@ -29,8 +29,7 @@
          r-bioc-biostrings,
          r-bioc-genomicranges,
          r-bioc-xvector
-Suggests: r-bioc-pasillabamsubset,
-          r-bioc-shortread
+Recommends: r-bioc-shortread
 Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import
  This package provides an interface to the 'samtools', 'bcftools', and
  'tabix' utilities for manipulating SAM (Sequence Alignment / Map),