[med-svn] r17538 - in trunk/packages/R/r-bioc-snpstats/trunk/debian: . tests

Andreas Tille tille at moszumanska.debian.org
Mon Jul 28 19:43:14 UTC 2014 

Author: tille
Date: 2014-07-28 19:43:14 +0000 (Mon, 28 Jul 2014)
New Revision: 17538

Added:
   trunk/packages/R/r-bioc-snpstats/trunk/debian/README.test
   trunk/packages/R/r-bioc-snpstats/trunk/debian/docs
   trunk/packages/R/r-bioc-snpstats/trunk/debian/examples
   trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/
   trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/control
   trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog
   trunk/packages/R/r-bioc-snpstats/trunk/debian/control
   trunk/packages/R/r-bioc-snpstats/trunk/debian/copyright
   trunk/packages/R/r-bioc-snpstats/trunk/debian/rules
   trunk/packages/R/r-bioc-snpstats/trunk/debian/watch
Log:
Delete zlib code from source package; add autopkgtest


Added: trunk/packages/R/r-bioc-snpstats/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/README.test	2014-07-28 19:43:14 UTC (rev 17538)
@@ -0,0 +1,5 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by loading it into R with the command
+‘library(snpStats)’ in order to confirm its integrity.

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog	2014-07-28 16:09:17 UTC (rev 17537)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/changelog	2014-07-28 19:43:14 UTC (rev 17538)
@@ -1,5 +1,11 @@
-r-bioc-snpstats (1.14.0-1) unstable; urgency=medium
+r-bioc-snpstats (1.14.0+dfsg-2) UNRELEASED; urgency=medium
 
+  * Add autopkgtest
+
+ -- Andreas Tille <tille at debian.org>  Mon, 28 Jul 2014 21:24:36 +0200
+
+r-bioc-snpstats (1.14.0+dfsg-1) unstable; urgency=medium
+
   * Initial release (closes: #756003)
 
  -- Andreas Tille <tille at debian.org>  Thu, 24 Jul 2014 09:03:52 +0200

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/control	2014-07-28 16:09:17 UTC (rev 17537)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/control	2014-07-28 19:43:14 UTC (rev 17538)
@@ -3,12 +3,14 @@
 Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
 Priority: optional
+Testsuite: autopkgtest
 Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,
                r-cran-survival,
                r-cran-matrix,
-               r-bioc-biocgenerics
+               r-bioc-biocgenerics,
+               zlib1g-dev
 Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-snpstats/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-snpstats/trunk/

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/copyright	2014-07-28 16:09:17 UTC (rev 17537)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/copyright	2014-07-28 19:43:14 UTC (rev 17538)
@@ -2,6 +2,32 @@
 Upstream-Name: snpStats
 Upstream-Contact: David Clayton <dc208 at cam.ac.uk> 
 Source: http://bioconductor.org/packages/release/bioc/html/snpStats.html
+Files-Excluded: src/adler32.c
+                src/compress.c
+                src/crc32.c
+                src/crc32.h
+                src/deflate.c
+                src/deflate.h
+                src/gzclose.c
+                src/gzguts.h
+                src/gzlib.c
+                src/gzread.c
+                src/gzwrite.c
+                src/infback.c
+                src/inffast.c
+                src/inffast.h
+                src/inffixed.h
+                src/inflate.c
+                src/inflate.h
+                src/inftrees.c
+                src/inftrees.h
+                src/trees.c
+                src/trees.h
+                src/uncompr.c
+                src/zconf.h
+                src/zlib.h
+                src/zutil.c
+                src/zutil.h
 
 Files: *
 Copyright: 2006-2014 David Clayton <dc208 at cam.ac.uk>
@@ -25,4 +51,4 @@
  along with this program.  If not, see <http://www.gnu.org/licenses/>
  .
  On Debian systems, the complete text of the GNU General Public
- License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’.
\ No newline at end of file
+ License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’.

Added: trunk/packages/R/r-bioc-snpstats/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/docs	2014-07-28 19:43:14 UTC (rev 17538)
@@ -0,0 +1 @@
+debian/README.test

Added: trunk/packages/R/r-bioc-snpstats/trunk/debian/examples
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/examples	                        (rev 0)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/examples	2014-07-28 19:43:14 UTC (rev 17538)
@@ -0,0 +1 @@
+vignettes

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/rules	2014-07-28 16:09:17 UTC (rev 17537)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/rules	2014-07-28 19:43:14 UTC (rev 17538)
@@ -2,3 +2,6 @@
 
 debRreposname=bioc
 include /usr/share/R/debian/r-cran.mk
+
+get-orig-source:
+	uscan --verbose --force-download --repack --compress xz

Added: trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/control	2014-07-28 19:43:14 UTC (rev 17538)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/tests/run-unit-test	2014-07-28 19:43:14 UTC (rev 17538)
@@ -0,0 +1,15 @@
+#!/bin/sh -e
+
+biocname=snpStats
+pkg=r-bioc-`echo $biocname | tr [A-Z] [a-z]`
+
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp /usr/share/doc/$pkg/examples/vignettes/* $ADTTMP
+gunzip *.gz
+R --no-save <<EOT
+Stangle("data-input-vignette.Rnw")
+source("data-input-vignette.R", echo=TRUE)
+EOT

Modified: trunk/packages/R/r-bioc-snpstats/trunk/debian/watch
===================================================================
--- trunk/packages/R/r-bioc-snpstats/trunk/debian/watch	2014-07-28 16:09:17 UTC (rev 17537)
+++ trunk/packages/R/r-bioc-snpstats/trunk/debian/watch	2014-07-28 19:43:14 UTC (rev 17538)
@@ -1,3 +1,3 @@
 version=3
-opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \
+opts=uversionmangle=s/$/+dfsg/,downloadurlmangle=s/\.\./packages\/release\/bioc/ \
  http://www.bioconductor.org/packages/release/bioc/html/snpStats.html .*/snpStats_([\d\.]+)\.tar\.gz

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