[med-svn] [r-bioc-ensembldb] 02/10: Update packaging for uploading to new

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository r-bioc-ensembldb.

commit 87c859bbd394646f6622ee1d5878b08dd3fc55b7
Author: Andreas Tille <tille at debian.org>
Date:   Tue May 31 10:14:51 2016 +0000

    Update packaging for uploading to new
---
 debian/README.test         | 10 ++++++++++
 debian/changelog           |  8 +++-----
 debian/control             |  6 ++++--
 debian/docs                |  1 +
 debian/lintian-overrides   |  2 ++
 debian/rules               |  3 +++
 debian/tests/control       |  3 +++
 debian/tests/run-unit-test |  5 +++++
 8 files changed, 31 insertions(+), 7 deletions(-)

diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..c6bf89f
--- /dev/null
+++ b/debian/README.test
@@ -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.
diff --git a/debian/changelog b/debian/changelog
index cb8566f..1e92f1b 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -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
diff --git a/debian/control b/debian/control
index 72b255a..2d6c1b5 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,8 @@ Priority: optional
 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 @@ Package: r-bioc-ensembldb
 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
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..50f6656
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1 @@
+debian/README.test
diff --git a/debian/lintian-overrides b/debian/lintian-overrides
new file mode 100644
index 0000000..3d55b14
--- /dev/null
+++ b/debian/lintian-overrides
@@ -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
diff --git a/debian/rules b/debian/rules
index aeb12b3..b6e9812 100755
--- a/debian/rules
+++ b/debian/rules
@@ -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
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..25377fc
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..5a0e2a1
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,5 @@
+#!/bin/sh -e
+
+LC_ALL=C R --no-save <<EOT
+BiocGenerics:::testPackage("ensembldb")
+EOT

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-ensembldb.git