[med-svn] r18332 - in trunk/packages/R/r-bioc-affy/trunk/debian: . patches tests

[Andreas Tille]

Author: tille
Date: 2014-10-17 20:51:13 +0000 (Fri, 17 Oct 2014)
New Revision: 18332

Modified:
   trunk/packages/R/r-bioc-affy/trunk/debian/changelog
   trunk/packages/R/r-bioc-affy/trunk/debian/control
   trunk/packages/R/r-bioc-affy/trunk/debian/patches/use_debian_packaged_zlib.patch
   trunk/packages/R/r-bioc-affy/trunk/debian/tests/run-unit-test
Log:
New upstream version and some polishing


Modified: trunk/packages/R/r-bioc-affy/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-affy/trunk/debian/changelog	2014-10-17 14:55:38 UTC (rev 18331)
+++ trunk/packages/R/r-bioc-affy/trunk/debian/changelog	2014-10-17 20:51:13 UTC (rev 18332)
@@ -1,3 +1,10 @@
+r-bioc-affy (1.44.0-1) experimental; urgency=medium
+
+  * New upstream version
+  * cme fix dpkg-copyright
+
+ -- Andreas Tille <tille at debian.org>  Thu, 16 Oct 2014 16:24:55 +0200
+
 r-bioc-affy (1.42.3-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-affy/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-affy/trunk/debian/control	2014-10-17 14:55:38 UTC (rev 18331)
+++ trunk/packages/R/r-bioc-affy/trunk/debian/control	2014-10-17 20:51:13 UTC (rev 18332)
@@ -2,17 +2,16 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
-Priority: optional
 Testsuite: autopkgtest
+Priority: optional
 Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,
-               r-bioc-biobase,
-               r-bioc-biocgenerics,
-               r-bioc-affyio,
-               r-bioc-biocinstaller,
-               r-bioc-preprocesscore
-Standards-Version: 3.9.5
+               r-bioc-biobase (>= 2.26.0),
+               r-bioc-affyio (>= 1.34.0),
+               r-bioc-biocinstaller (>= 1.16.0),
+               r-bioc-preprocesscore (>= 1.28.0)
+Standards-Version: 3.9.6
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-affy/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-affy/trunk/
 Homepage: http://bioconductor.org/packages/release/bioc/html/affy.html
@@ -22,11 +21,10 @@
 Depends: ${R:Depends},
          ${misc:Depends},
          ${shlibs:Depends},
-         r-bioc-biobase,
-         r-bioc-biocgenerics,
-         r-bioc-affyio,
-         r-bioc-biocinstaller,
-         r-bioc-preprocesscore
+         r-bioc-biobase (>= 2.26.0),
+         r-bioc-affyio (>= 1.34.0),
+         r-bioc-biocinstaller (>= 1.16.0),
+         r-bioc-preprocesscore (>= 1.28.0)
 Description: BioConductor methods for Affymetrix Oligonucleotide Arrays
  This is part of the BioConductor GNU R suite.  The package contains
  functions for exploratory oligonucleotide array analysis. 

Modified: trunk/packages/R/r-bioc-affy/trunk/debian/patches/use_debian_packaged_zlib.patch
===================================================================
--- trunk/packages/R/r-bioc-affy/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-10-17 14:55:38 UTC (rev 18331)
+++ trunk/packages/R/r-bioc-affy/trunk/debian/patches/use_debian_packaged_zlib.patch	2014-10-17 20:51:13 UTC (rev 18332)
@@ -3,9 +3,9 @@
 Description: If the systems includes zlib natively there is no point in
  requiring the import of zlibbioc
 
---- affy.orig/DESCRIPTION
-+++ affy/DESCRIPTION
-@@ -13,7 +13,7 @@
+--- a/DESCRIPTION
++++ b/DESCRIPTION
+@@ -13,7 +13,7 @@ Author: Rafael A. Irizarry <rafa at jhu.edu
  Maintainer: Rafael A. Irizarry <rafa at jhu.edu>
  Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)
  Imports: affyio (>= 1.13.3), BiocInstaller, graphics, grDevices,
@@ -14,9 +14,9 @@
  Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools
  LinkingTo: preprocessCore
  Description: The package contains functions for exploratory
---- affy.orig/NAMESPACE
-+++ affy/NAMESPACE
-@@ -4,8 +4,6 @@
+--- a/NAMESPACE
++++ b/NAMESPACE
+@@ -4,8 +4,6 @@ importFrom(BiocGenerics, updateObject, c
  
  import(affyio)
  

Modified: trunk/packages/R/r-bioc-affy/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-affy/trunk/debian/tests/run-unit-test	2014-10-17 14:55:38 UTC (rev 18331)
+++ trunk/packages/R/r-bioc-affy/trunk/debian/tests/run-unit-test	2014-10-17 20:51:13 UTC (rev 18332)
@@ -1,11 +1,13 @@
 #!/bin/sh -e
 
-pkg=r-bioc-affy
+oname=affy
+pkg=r-bioc-`echo $oname | tr [A-Z] [a-z]`
 if [ "$ADTTMP" = "" ] ; then
   ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
 fi
 cd $ADTTMP
-cp /usr/lib/R/site-library/affy/tests/* $ADTTMP
+cp -a /usr/lib/R/site-library/${oname}/tests/* $ADTTMP
+find . -name "*.gz" -exec gunzip \{\} \;
 for runtest in `ls *.R` ; do
     if ! grep -wq affydata $runtest ; then
 	R --no-save < $runtest