[med-svn] r18378 - in trunk/packages/R/r-bioc-genomicfeatures/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2014-10-23 07:07:32 +0000 (Thu, 23 Oct 2014)
New Revision: 18378

Modified:
   trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test
   trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/changelog
   trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/control
   trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/tests/run-unit-test
Log:
New upstream version, add hint why tests might fail after changes at ensembl database


Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test	2014-10-23 06:35:52 UTC (rev 18377)
+++ trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/README.test	2014-10-23 07:07:32 UTC (rev 18378)
@@ -28,4 +28,27 @@
 original files from inst/unitTests to the installation directory or you
 rebuild this package by deactivating the patch in the series file.
 
+Further important note why it might happen that some tests might fail
+[see for complete mail test the Debian Med mailing list archive
+ http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-October/030474.html]:
+
+  Date: Wed, 22 Oct 2014 10:41:45 -0700
+  From: Marc Carlson <mcarlson at fhcrc.org>
+  Subject: Re: [devteam-bioc] Failed test in GenomicFeatures
+  
+  Hi Andreas,
+  
+  This is something that can happen whenever data sources at ensembl are
+  updated causing our test of the real ensembl data to become
+  temporarily invalid.  We have already updated out packages to reflect
+  the new data coming from ensembl.  You can see the build report here:
+  
+  http://www.bioconductor.org/checkResults/3.0/bioc-LATEST/
+  
+  And the latest released version of this software is also described
+  (and available) here:
+  
+  http://www.bioconductor.org/packages/3.0/bioc/html/GenomicFeatures.html
+
+
  -- Andreas Tille <tille at debian.org>  Thu, 24 Jul 2014 08:35:54 +0200

Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/changelog	2014-10-23 06:35:52 UTC (rev 18377)
+++ trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/changelog	2014-10-23 07:07:32 UTC (rev 18378)
@@ -1,6 +1,12 @@
-r-bioc-genomicfeatures (1.18.0-1) UNRELEASED; urgency=medium
+r-bioc-genomicfeatures (1.18.1-1) experimental; urgency=medium
 
   * New upstream version
+
+ -- Andreas Tille <tille at debian.org>  Thu, 23 Oct 2014 08:32:04 +0200
+
+r-bioc-genomicfeatures (1.18.0-1) experimental; urgency=medium
+
+  * New upstream version
   * Updated versioned dependencies
 
  -- Andreas Tille <tille at debian.org>  Tue, 21 Oct 2014 05:14:22 +0200

Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/control	2014-10-23 06:35:52 UTC (rev 18377)
+++ trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/control	2014-10-23 07:07:32 UTC (rev 18378)
@@ -9,8 +9,6 @@
                r-base-dev,
                r-cran-dbi,
                r-cran-rsqlite,
-               r-bioc-biostrings (>= 2.34.0),
-               r-bioc-genomicranges (>= 1.18.1),
                r-bioc-biomart (>= 2.22.0),
                r-bioc-rtracklayer (>= 1.26.0)
 Standards-Version: 3.9.6
@@ -23,8 +21,6 @@
 Depends: ${R:Depends},
          ${misc:Depends},
          r-cran-rsqlite,
-         r-bioc-biostrings (>= 2.34.0),
-         r-bioc-genomicranges (>= 1.18.1),
          r-bioc-biomart (>= 2.22.0),
          r-bioc-rtracklayer (>= 1.26.0)
 Description: GNU R tools for making and manipulating transcript centric annotations

Modified: trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/tests/run-unit-test	2014-10-23 06:35:52 UTC (rev 18377)
+++ trunk/packages/R/r-bioc-genomicfeatures/trunk/debian/tests/run-unit-test	2014-10-23 07:07:32 UTC (rev 18378)
@@ -1,5 +1,8 @@
 #!/bin/sh -e
 
+# Some test might fail due to changes in ensembl data sources
+# see http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-October/030474.html
+
 LC_ALL=C R --no-save <<EOT
 require("GenomicFeatures")
 GenomicFeatures:::.test()