[med-svn] r17190 - in trunk/packages/R/r-bioc-rsamtools/trunk/debian: . patches tests

[Andreas Tille]

Author: tille
Date: 2014-06-16 21:29:30 +0000 (Mon, 16 Jun 2014)
New Revision: 17190

Added:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/control
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
   trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
Add unittest which currently fails.  See what might happen if dependencies will be up to date


Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2014-06-16 21:26:28 UTC (rev 17189)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog	2014-06-16 21:29:30 UTC (rev 17190)
@@ -1,3 +1,15 @@
+r-bioc-rsamtools (1.16.1-1) unstable; urgency=medium
+
+  * New upstream version
+  * Add autopkgtest
+TODO:
+Need to wait for latest versions of dependencies since test currently fails
+  * cme fix dpkg-control
+  * Bumped Dependencies of packages needed in test suite from
+    Suggests to Recommends
+
+ -- Andreas Tille <tille at debian.org>  Mon, 16 Jun 2014 16:28:55 +0200
+
 r-bioc-rsamtools (1.14.2-1) unstable; urgency=low
 
   * New upstream version (adapted patch)

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2014-06-16 21:26:28 UTC (rev 17189)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/control	2014-06-16 21:29:30 UTC (rev 17190)
@@ -2,6 +2,7 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
+Testsuite: autopkgtest
 Priority: optional
 Build-Depends: debhelper (>= 9),
                cdbs,
@@ -13,7 +14,7 @@
                r-bioc-genomicranges,
                r-bioc-xvector,
                libbam-dev
-Standards-Version: 3.9.4
+Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/
 Homepage: http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html
@@ -29,8 +30,8 @@
          r-bioc-biostrings,
          r-bioc-genomicranges,
          r-bioc-xvector
-# The following BioConductor modules are not yet packaged but used in the unit test
-Suggests: r-bioc-pasillabamsubset, r-bioc-shortread
+Recommends: r-bioc-pasillabamsubset,
+            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),

Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-06-16 21:26:28 UTC (rev 17189)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-06-16 21:29:30 UTC (rev 17190)
@@ -5,13 +5,13 @@
 
 --- a/DESCRIPTION
 +++ b/DESCRIPTION
-@@ -14,7 +14,7 @@ License: Artistic-2.0 | file LICENSE
- LazyLoad: yes
- Depends: methods, IRanges (>= 1.19.11), GenomicRanges (>= 1.13.35),
-         XVector, Biostrings (>= 2.29.7)
+@@ -15,7 +15,7 @@ LazyLoad: yes
+ Depends: methods, IRanges (>= 1.21.10), GenomicRanges (>= 1.15.11),
+         XVector (>= 0.3.2), Biostrings (>= 2.31.3), GenomeInfoDb(>=
+         0.99.17)
 -Imports: utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops
 +Imports: utils, BiocGenerics (>= 0.1.3), bitops
- Suggests: ShortRead (>= 1.19.10), GenomicFeatures,
+ Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures,
          TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db,
          TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14,
 --- a/NAMESPACE

Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/control	2014-06-16 21:29:30 UTC (rev 17190)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-runit, r-bioc-pasillabamsubset, r-bioc-shortread
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/tests/run-unit-test	2014-06-16 21:29:30 UTC (rev 17190)
@@ -0,0 +1,6 @@
+#!/bin/sh -e
+
+LC_ALL=C R --no-save <<EOT
+BiocGenerics:::testPackage('Rsamtools')
+EOT
+