[med-svn] r22051 - in trunk/packages/R/r-bioc-ensembldb/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2016-05-31 10:14:51 +0000 (Tue, 31 May 2016)
New Revision: 22051

Added:
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/README.test
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/docs
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/lintian-overrides
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/control
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/changelog
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/control
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/rules
Log:
Update packaging for uploading to new


Added: trunk/packages/R/r-bioc-ensembldb/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/README.test	                        (rev 0)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/README.test	2016-05-31 10:14:51 UTC (rev 22051)
@@ -0,0 +1,10 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+LC_ALL=C R --no-save <<EOT
+BiocGenerics:::testPackage("ensembldb")
+EOT
+
+in order to confirm its integrity.

Modified: trunk/packages/R/r-bioc-ensembldb/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/changelog	2016-05-30 10:39:52 UTC (rev 22050)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/changelog	2016-05-31 10:14:51 UTC (rev 22051)
@@ -1,7 +1,5 @@
-r-bioc-ensembldb (1.4.0-1) UNRELEASED; urgency=low
+r-bioc-ensembldb (1.4.3-1) unstable; urgency=low
 
-  * Initial release (closes: #???)
-    TODO:
-        svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-annotationhub/trunk/
+  * Initial release (closes: #825906)
 
- -- Andreas Tille <tille at debian.org>  Wed, 11 May 2016 15:29:00 +0200
+ -- Andreas Tille <tille at debian.org>  Tue, 31 May 2016 11:41:29 +0200

Modified: trunk/packages/R/r-bioc-ensembldb/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/control	2016-05-30 10:39:52 UTC (rev 22050)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/control	2016-05-31 10:14:51 UTC (rev 22051)
@@ -6,7 +6,8 @@
 Build-Depends: debhelper (>= 9),
                cdbs,
                r-base-dev,
-               r-bioc-genomicfeatures
+               r-bioc-genomicfeatures,
+               r-bioc-annotationhub
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-ensembldb/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-ensembldb/trunk/
@@ -16,7 +17,8 @@
 Architecture: all
 Depends: ${R:Depends},
          ${misc:Depends},
-         r-bioc-genomicfeatures
+         r-bioc-genomicfeatures,
+         r-bioc-annotationhub
 Description: GNU R utilities to create and use an Ensembl based annotation database
  The package provides functions to create and use transcript centric
  annotation databases/packages. The annotation for the databases are

Added: trunk/packages/R/r-bioc-ensembldb/trunk/debian/docs
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/docs	2016-05-31 10:14:51 UTC (rev 22051)
@@ -0,0 +1 @@
+debian/README.test

Added: trunk/packages/R/r-bioc-ensembldb/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/lintian-overrides	                        (rev 0)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/lintian-overrides	2016-05-31 10:14:51 UTC (rev 22051)
@@ -0,0 +1,2 @@
+# Same file as in source tarball is installed in binary - this does not affect reproducible builds
+r-bioc-ensembldb: package-contains-timestamped-gzip usr/lib/R/site-library/ensembldb/txt/ENST000*.fa.gz

Modified: trunk/packages/R/r-bioc-ensembldb/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/rules	2016-05-30 10:39:52 UTC (rev 22050)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/rules	2016-05-31 10:14:51 UTC (rev 22051)
@@ -2,3 +2,6 @@
 
 debRreposname=bioc
 include /usr/share/R/debian/r-cran.mk
+
+install/$(package)::
+	chmod a+x $(debRlib)/$(cranName)/perl/get_gene_transcript_exon_tables.pl

Added: trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/control	2016-05-31 10:14:51 UTC (rev 22051)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr

Added: trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/tests/run-unit-test	2016-05-31 10:14:51 UTC (rev 22051)
@@ -0,0 +1,5 @@
+#!/bin/sh -e
+
+LC_ALL=C R --no-save <<EOT
+BiocGenerics:::testPackage("ensembldb")
+EOT