[med-svn] r22945 - trunk/packages/R/r-bioc-ensembldb/trunk/debian

[Andreas Tille]

Author: tille
Date: 2016-10-27 13:32:42 +0000 (Thu, 27 Oct 2016)
New Revision: 22945

Removed:
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/lintian-overrides
Modified:
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/README.test
   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/copyright
   trunk/packages/R/r-bioc-ensembldb/trunk/debian/rules
Log:
  * New upstream version
  * Convert to dh-r
  * Generic BioConductor homepage
  * Exclude tests requiring EnsDb.Hsapiens.v75 from unit tests



Modified: trunk/packages/R/r-bioc-ensembldb/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/README.test	2016-10-27 13:00:15 UTC (rev 22944)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/README.test	2016-10-27 13:32:42 UTC (rev 22945)
@@ -7,4 +7,7 @@
 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.

Modified: trunk/packages/R/r-bioc-ensembldb/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/changelog	2016-10-27 13:00:15 UTC (rev 22944)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/changelog	2016-10-27 13:32:42 UTC (rev 22945)
@@ -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)

Modified: trunk/packages/R/r-bioc-ensembldb/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/control	2016-10-27 13:00:15 UTC (rev 22944)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/control	2016-10-27 13:32:42 UTC (rev 22945)
@@ -4,21 +4,21 @@
 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

Modified: trunk/packages/R/r-bioc-ensembldb/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/copyright	2016-10-27 13:00:15 UTC (rev 22944)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/copyright	2016-10-27 13:32:42 UTC (rev 22945)
@@ -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>,

Deleted: trunk/packages/R/r-bioc-ensembldb/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/lintian-overrides	2016-10-27 13:00:15 UTC (rev 22944)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/lintian-overrides	2016-10-27 13:32:42 UTC (rev 22945)
@@ -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

Modified: trunk/packages/R/r-bioc-ensembldb/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-ensembldb/trunk/debian/rules	2016-10-27 13:00:15 UTC (rev 22944)
+++ trunk/packages/R/r-bioc-ensembldb/trunk/debian/rules	2016-10-27 13:32:42 UTC (rev 22945)
@@ -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