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 <[email protected]> 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 <[email protected]> -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 <[email protected]> +Copyright: 2013-2016 Andreas Tille <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
