Author: tille Date: 2015-11-06 10:56:51 +0000 (Fri, 06 Nov 2015) New Revision: 20406
Added: trunk/packages/R/r-bioc-shortread/trunk/debian/lintian-overrides Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/changelog trunk/packages/R/r-bioc-shortread/trunk/debian/control trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch trunk/packages/R/r-bioc-shortread/trunk/debian/watch Log: New upstream version, ignore false lintian positives Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/changelog =================================================================== --- trunk/packages/R/r-bioc-shortread/trunk/debian/changelog 2015-11-06 10:53:49 UTC (rev 20405) +++ trunk/packages/R/r-bioc-shortread/trunk/debian/changelog 2015-11-06 10:56:51 UTC (rev 20406) @@ -1,3 +1,10 @@ +r-bioc-shortread (1.28.0-1) unstable; urgency=medium + + * New upstream version + * Ignore false positive lintian warnings + + -- Andreas Tille <[email protected]> Fri, 06 Nov 2015 08:59:35 +0100 + r-bioc-shortread (1.26.0-1) unstable; urgency=medium * New upstream version Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/control =================================================================== --- trunk/packages/R/r-bioc-shortread/trunk/debian/control 2015-11-06 10:53:49 UTC (rev 20405) +++ trunk/packages/R/r-bioc-shortread/trunk/debian/control 2015-11-06 10:56:51 UTC (rev 20406) @@ -9,7 +9,7 @@ r-base-dev, r-cran-latticeextra, r-bioc-biobase (>= 2.26.0), - r-bioc-genomicalignments (>= 1.4.1), + r-bioc-genomicalignments (>= 1.6.0), r-cran-hwriter Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-shortread/trunk/ @@ -23,7 +23,7 @@ ${shlibs:Depends}, r-cran-latticeextra, r-bioc-biobase (>= 2.26.0), - r-bioc-genomicalignments (>= 1.4.1), + r-bioc-genomicalignments (>= 1.6.0), r-cran-hwriter Description: GNU R classes and methods for high-throughput short-read sequencing data This BioConductor module is a package for input, quality assessment, Added: trunk/packages/R/r-bioc-shortread/trunk/debian/lintian-overrides =================================================================== --- trunk/packages/R/r-bioc-shortread/trunk/debian/lintian-overrides (rev 0) +++ trunk/packages/R/r-bioc-shortread/trunk/debian/lintian-overrides 2015-11-06 10:56:51 UTC (rev 20406) @@ -0,0 +1,3 @@ +# Ignore false positives that are just plain copies of the gz archives in upstream tarball +r-bioc-shortread: package-contains-timestamped-gzip usr/lib/R/site-library/ShortRead/extdata/E-MTAB-1147/.* +r-bioc-shortread: package-contains-timestamped-gzip usr/lib/R/site-library/ShortRead/unitTests/cases/PE_export.txt.gz Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch =================================================================== --- trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch 2015-11-06 10:53:49 UTC (rev 20405) +++ trunk/packages/R/r-bioc-shortread/trunk/debian/patches/use_debian_packaged_zlib.patch 2015-11-06 10:56:51 UTC (rev 20406) @@ -4,17 +4,6 @@ Description: If the systems includes zlib natively there is no point in requiring the import of zlibbioc ---- a/DESCRIPTION -+++ b/DESCRIPTION -@@ -18,7 +18,7 @@ Depends: BiocGenerics (>= 0.11.3), BiocP - 2.33.14), Rsamtools (>= 1.17.28), GenomicAlignments (>= 1.1.28) - Imports: Biobase, S4Vectors (>= 0.5.11), IRanges (>= 1.99.27), - GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.17.39), hwriter, -- methods, zlibbioc, lattice, latticeExtra, -+ methods, lattice, latticeExtra, - Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi - LinkingTo: S4Vectors, IRanges, XVector, Biostrings - biocViews: DataImport, Sequencing, QualityControl --- a/NAMESPACE +++ b/NAMESPACE @@ -1,6 +1,6 @@ @@ -25,3 +14,14 @@ Biostrings, GenomeInfoDb, GenomicRanges, GenomicAlignments, Rsamtools, Biobase) +--- a/DESCRIPTION ++++ b/DESCRIPTION +@@ -18,7 +18,7 @@ Depends: BiocGenerics (>= 0.11.3), BiocP + 2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4) + Imports: Biobase, S4Vectors (>= 0.7.1), IRanges (>= 2.3.7), + GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.21.6), hwriter, +- methods, zlibbioc, lattice, latticeExtra, ++ methods, lattice, latticeExtra, + Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi + LinkingTo: S4Vectors, IRanges, XVector, Biostrings + biocViews: DataImport, Sequencing, QualityControl Modified: trunk/packages/R/r-bioc-shortread/trunk/debian/watch =================================================================== --- trunk/packages/R/r-bioc-shortread/trunk/debian/watch 2015-11-06 10:53:49 UTC (rev 20405) +++ trunk/packages/R/r-bioc-shortread/trunk/debian/watch 2015-11-06 10:56:51 UTC (rev 20406) @@ -1,3 +1,3 @@ version=3 -opts=downloadurlmangle=s/\.\./packages\/release\/bioc/ \ +opts=downloadurlmangle=s?^(.*)\.\.?http:$1packages/release/bioc? \ http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html .*/ShortRead_([\d\.]+)\.tar\.gz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
