[med-svn] r17189 - in trunk/packages/R/r-bioc-shortread/trunk/debian: . patches tests

[Andreas Tille]

Author: tille
Date: 2014-06-16 21:26:28 +0000 (Mon, 16 Jun 2014)
New Revision: 17189

Added:
   trunk/packages/R/r-bioc-shortread/trunk/debian/tests/
   trunk/packages/R/r-bioc-shortread/trunk/debian/tests/control
   trunk/packages/R/r-bioc-shortread/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-shortread/trunk/debian/README.test
   trunk/packages/R/r-bioc-shortread/trunk/debian/changelog
   trunk/packages/R/r-bioc-shortread/trunk/debian/control
   trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch
Log:
Add autopkgtest, needs new dependencies we need to wait for


Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/README.test	2014-06-16 21:09:51 UTC (rev 17188)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/README.test	2014-06-16 21:26:28 UTC (rev 17189)
@@ -1,5 +1,11 @@
 Notes on how this package can be tested.
 ────────────────────────────────────────
 
-This package can be tested by loading it into R with the command
-‘library(ShortRead)’ in order to confirm its integrity.
+This package can be tested by running the provided test:
+
+LC_ALL=C R --no-save <<EOT
+require("ShortRead") || stop("unable to load ShortRead package")
+ShortRead:::.test()
+EOT
+
+in order to confirm its integrity.

Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/changelog	2014-06-16 21:09:51 UTC (rev 17188)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/changelog	2014-06-16 21:26:28 UTC (rev 17189)
@@ -1,7 +1,11 @@
-r-bioc-shortread (1.22.0-1) UNRELEASED; urgency=medium
+r-bioc-shortread (1.22.0-1) unstable; urgency=medium
 
   * New upstream version
   * Moved debian/upstream to debian/upstream/metadata
+  * Add autopkgtest
+  TODO: Needs
+     svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicalignments/trunk/
+     svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-biocparallel/trunk/
 
  -- Andreas Tille <tille at debian.org>  Mon, 16 Jun 2014 23:08:56 +0200
 

Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/control	2014-06-16 21:09:51 UTC (rev 17188)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/control	2014-06-16 21:26:28 UTC (rev 17189)
@@ -3,6 +3,7 @@
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
 Priority: optional
+Testsuite: autopkgtest
 Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,

Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-06-16 21:09:51 UTC (rev 17188)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-06-16 21:26:28 UTC (rev 17189)
@@ -4,19 +4,19 @@
 Description: If the systems includes zlib natively there is no point in
  requiring the import of zlibbioc
 
---- a/DESCRIPTION
-+++ b/DESCRIPTION
-@@ -13,7 +13,7 @@ LazyLoad: yes
- Depends: methods, BiocGenerics (>= 0.1.0), IRanges (>= 1.19.34),
-         GenomicRanges (>= 1.13.43), Biostrings (>= 2.29.18), lattice,
-         Rsamtools (>= 1.13.1)
--Imports: Biobase, hwriter, zlibbioc, latticeExtra
-+Imports: Biobase, hwriter, latticeExtra
- Enhances: Rmpi, parallel
- Suggests: biomaRt, RUnit, GenomicFeatures, yeastNagalakshmi
+--- ShortRead.orig/DESCRIPTION
++++ ShortRead/DESCRIPTION
+@@ -17,7 +17,7 @@
+ Depends: BiocGenerics (>= 0.1.0), BiocParallel, Biostrings (>=
+         2.31.14), Rsamtools (>= 1.13.1), GenomicAlignments (>= 0.99.6)
+ Imports: Biobase, GenomicRanges (>= 1.15.26), IRanges (>= 1.21.22),
+-        hwriter, methods, zlibbioc, lattice, latticeExtra,
++        hwriter, methods, lattice, latticeExtra,
+ Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
  LinkingTo: IRanges, XVector, Biostrings
---- a/NAMESPACE
-+++ b/NAMESPACE
+ biocViews: DataImport, Sequencing, QualityControl
+--- ShortRead.orig/NAMESPACE
++++ ShortRead/NAMESPACE
 @@ -1,7 +1,5 @@
  useDynLib(ShortRead, .registration=TRUE)
  

Added: trunk/packages/R/r-bioc-shortread/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/tests/control	2014-06-16 21:26:28 UTC (rev 17189)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-shortread/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-shortread/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-shortread/trunk/debian/tests/run-unit-test	2014-06-16 21:26:28 UTC (rev 17189)
@@ -0,0 +1,7 @@
+#!/bin/sh -e
+
+LC_ALL=C R --no-save <<EOT
+require("ShortRead")
+ShortRead:::.test()
+EOT
+