[med-svn] [r-bioc-ensembldb] 04/10: * New upstream version * Convert to dh-r * Generic BioConductor homepage * Exclude tests requiring EnsDb.Hsapiens.v75 from unit tests

[Andreas Tille]

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

commit 1ab7d483ae9a120b3b1efefeab1a2b5e4e2564d4
Author: Andreas Tille <tille at debian.org>
Date:   Thu Oct 27 13:32:42 2016 +0000

      * New upstream version
      * Convert to dh-r
      * Generic BioConductor homepage
      * Exclude tests requiring EnsDb.Hsapiens.v75 from unit tests
---
 debian/README.test       |  5 ++++-
 debian/changelog         |  9 +++++++++
 debian/control           |  8 ++++----
 debian/copyright         |  4 ++--
 debian/lintian-overrides |  2 --
 debian/rules             | 22 ++++++++++++++++++----
 6 files changed, 37 insertions(+), 13 deletions(-)

diff --git a/debian/README.test b/debian/README.test
index c6bf89f..bb496c4 100644
--- a/debian/README.test
+++ b/debian/README.test
@@ -7,4 +7,7 @@ LC_ALL=C R --no-save <<EOT
 BiocGenerics:::testPackage("ensembldb")
 EOT
 
-in order to confirm its integrity.
+in order to confirm its integrity.  However, to successfully run this
+testsuite you need to install the EnsDb.Hsapiens.v75 BioConductor
+databases.  It was decided that creating Debian packages of large size
+just to run the test suite is not very sensible.
diff --git a/debian/changelog b/debian/changelog
index f31299f..c12bc51 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,12 @@
+r-bioc-ensembldb (1.6.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * Convert to dh-r
+  * Generic BioConductor homepage
+  * Exclude tests requiring EnsDb.Hsapiens.v75 from unit tests
+
+ -- Andreas Tille <tille at debian.org>  Thu, 27 Oct 2016 14:39:59 +0200
+
 r-bioc-ensembldb (1.4.6-1) unstable; urgency=low
 
   * Initial release (closes: #825906)
diff --git a/debian/control b/debian/control
index 2d6c1b5..3ca691b 100644
--- a/debian/control
+++ b/debian/control
@@ -4,21 +4,21 @@ Uploaders: Andreas Tille <tille at debian.org>
 Section: gnu-r
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               cdbs,
+               dh-r,
                r-base-dev,
                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/
-Homepage: http://bioconductor.org/packages/release/bioc/html/ensembldb.html
+Homepage: https://bioconductor.org/packages/ensembldb/
 
 Package: r-bioc-ensembldb
 Architecture: all
 Depends: ${R:Depends},
          ${misc:Depends},
-         r-bioc-genomicfeatures,
-         r-bioc-annotationhub
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
 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/copyright b/debian/copyright
index 08a98f1..08c8a37 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,7 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: ensembldb
 Upstream-Contact: Johannes Rainer <johannes.rainer at eurac.edu> 
-Source: http://bioconductor.org/packages/release/bioc/html/ensembldb.html
+Source: https://bioconductor.org/packages/ensembldb/
 
 Files: *
 Copyright: 2006-2016 Johannes Rainer <johannes.rainer at eurac.edu>,
diff --git a/debian/lintian-overrides b/debian/lintian-overrides
deleted file mode 100644
index 3d55b14..0000000
--- a/debian/lintian-overrides
+++ /dev/null
@@ -1,2 +0,0 @@
-# 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 b6e9812..1355319 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,7 +1,21 @@
 #!/usr/bin/make -f
 
-debRreposname=bioc
-include /usr/share/R/debian/r-cran.mk
+debRreposname   := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}' | sed 's/r-\([a-z]\+\)-.*/\1/')
+awkString       := "'/^(Package|Bundle):/ {print $$2 }'"
+cranNameOrig    := $(shell awk "$(awkString)" DESCRIPTION)
+cranName        := $(shell echo "$(cranNameOrig)" | tr A-Z a-z)
+package         := r-$(debRreposname)-$(cranName)
+debRdir         := usr/lib/R/site-library
+debRlib         := $(CURDIR)/debian/$(package)/$(debRdir)
 
-install/$(package)::
-	chmod a+x $(debRlib)/$(cranName)/perl/get_gene_transcript_exon_tables.pl
+%:
+	dh $@ --buildsystem R
+
+override_dh_fixperms:
+	dh_fixperms
+	find debian -name "*.pl" -exec chmod +x \{\} \;
+
+# remove those unit tests that are requiring EnsDb.Hsapiens.v75
+override_dh_install:
+	dh_install
+	for tst in `grep -H -l 'library(.*EnsDb.Hsapiens.v75.*)' $(debRlib)/$(cranNameOrig)/unitTests/test_*.R` ; do rm -f $${tst} ; done

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