[med-svn] r22980 - in trunk/packages/R/r-bioc-genomicalignments/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-10-31 08:50:38 +0000 (Mon, 31 Oct 2016)
New Revision: 22980

Modified:
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/copyright
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch
   trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules
Log:
  * New upstream version
  * Convert to dh-r
  * Generic BioConductor homepage



Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog	2016-10-31 08:49:37 UTC (rev 22979)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/changelog	2016-10-31 08:50:38 UTC (rev 22980)
@@ -1,3 +1,11 @@
+r-bioc-genomicalignments (1.10.0-1) unstable; urgency=medium
+
+  * New upstream version
+  * Convert to dh-r
+  * Generic BioConductor homepage
+
+ -- Andreas Tille <tille at debian.org>  Wed, 26 Oct 2016 22:07:07 +0200
+
 r-bioc-genomicalignments (1.8.0-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control	2016-10-31 08:49:37 UTC (rev 22979)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/control	2016-10-31 08:50:38 UTC (rev 22980)
@@ -4,24 +4,22 @@
 Section: gnu-r
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               cdbs,
+               dh-r,
                r-base-dev,
                r-bioc-rsamtools (>= 1.22.0),
                r-bioc-summarizedexperiment
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomicalignments/trunk/
 Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicalignments/trunk/
-Homepage: http://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html
+Homepage: https://bioconductor.org/packages/GenomicAlignments/
 
 Package: r-bioc-genomicalignments
 Architecture: any
 Depends: ${R:Depends},
          ${misc:Depends},
          ${shlibs:Depends},
-         r-bioc-rsamtools (>= 1.22.0),
-         r-bioc-summarizedexperiment,
-         r-bioc-genomicranges (>= 1.22.4)
-Recommends: r-bioc-shortread
+Recommends: ${R:Recommends}
+Suggests: ${R:Suggests}
 Description: BioConductor representation and manipulation of short genomic alignments
  This BioConductor package provides efficient containers for storing and
  manipulating short genomic alignments (typically obtained by aligning

Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/copyright
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/copyright	2016-10-31 08:49:37 UTC (rev 22979)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/copyright	2016-10-31 08:50:38 UTC (rev 22980)
@@ -1,14 +1,14 @@
-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: GenomicAlignments
 Upstream-Contact: Bioconductor Package Maintainer <maintainer at bioconductor.org>
-Source: http://bioconductor.org/packages/release/bioc/html/GenomicAlignments.html
+Source: https://bioconductor.org/packages/GenomicAlignments/
 
 Files: *
-Copyright: © 2006-2014 Hervè Pagès, Valerie Obenchain, Martin Morgan 
+Copyright: © 2006-2016 Hervè Pagès, Valerie Obenchain, Martin Morgan 
 License: Artistic-2.0
 
 Files: debian/*
-Copyright: 2013 Andreas Tille <tille at debian.org>
+Copyright: 2013-2016 Andreas Tille <tille at debian.org>
 License: Artistic-2.0
 
 License: Artistic-2.0

Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch	2016-10-31 08:49:37 UTC (rev 22979)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/patches/disable-testing-pasillaBamSubset.patch	2016-10-31 08:50:38 UTC (rev 22980)
@@ -8,7 +8,7 @@
 
 --- a/inst/unitTests/test_readGAlignmentsList.R
 +++ /dev/null
-@@ -1,189 +0,0 @@
+@@ -1,184 +0,0 @@
 -library(pasillaBamSubset)
 -chr4 <- untreated3_chr4()
 -
@@ -77,16 +77,11 @@
 -    galist <- readGAlignmentsList(bamfile)
 -    mates <- galist[mcols(galist)$mate_status == "mated"]
 -    galp <- readGAlignmentPairs(bamfile)
--    checkIdentical(length(galp), 75346L)
+-    checkIdentical(length(galp), 75409L)
 -    tbl <- table(mcols(galist))
 -    checkIdentical(tbl[["mated"]], 75409L)
 -    checkIdentical(tbl[["ambiguous"]], 0L)
 -    checkIdentical(tbl[["unmated"]], 21227L)
--
--    ## GAlignmentPairs holds concordant (opposite strand) pairs
--    samestrand <- galist[elementNROWS(runValue(strand(galist))) == 1L]
--    samestrandp <- sum(mcols(samestrand)$mate_status == "mated")
--    checkIdentical(tbl[["mated"]] - samestrandp, length(galp))
 -}
 -
 -test_readGAlignmentsList_flags <- function()

Modified: trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules	2016-10-31 08:49:37 UTC (rev 22979)
+++ trunk/packages/R/r-bioc-genomicalignments/trunk/debian/rules	2016-10-31 08:50:38 UTC (rev 22980)
@@ -1,7 +1,4 @@
 #!/usr/bin/make -f
 
-debRreposname=bioc
-include /usr/share/R/debian/r-cran.mk
-
-clean::
-	rm -f src/*.so
+%:
+	dh $@ --buildsystem R