Author: tille Date: 2015-10-31 18:28:47 +0000 (Sat, 31 Oct 2015) New Revision: 20365
Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog trunk/packages/R/r-bioc-rsamtools/trunk/debian/control trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch Log: New upstream version, (Build-)Depends: r-bioc-biocparallel Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog =================================================================== --- trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog 2015-10-31 08:12:02 UTC (rev 20364) +++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/changelog 2015-10-31 18:28:47 UTC (rev 20365) @@ -1,3 +1,11 @@ +r-bioc-rsamtools (1.22.0-1) unstable; urgency=medium + + * New upstream version + * (Build-)Depends: r-bioc-biocparallel + * Add lintian-override for false positive + + -- Andreas Tille <[email protected]> Fri, 30 Oct 2015 14:05:41 +0100 + r-bioc-rsamtools (1.20.4-1) unstable; urgency=medium * New upstream version Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/control =================================================================== --- trunk/packages/R/r-bioc-rsamtools/trunk/debian/control 2015-10-31 08:12:02 UTC (rev 20364) +++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/control 2015-10-31 18:28:47 UTC (rev 20365) @@ -7,8 +7,9 @@ cdbs, r-base-dev, r-cran-bitops, - r-bioc-biostrings (>= 2.34.0), - r-bioc-genomicranges (>= 1.18.0), + r-bioc-biostrings (>= 2.38.0), + r-bioc-genomicranges (>= 1.22.0), + r-bioc-biocparallel, libbam-dev Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-rsamtools/trunk/ @@ -22,7 +23,8 @@ ${shlibs:Depends}, r-cran-bitops, r-bioc-biostrings (>= 2.34.0), - r-bioc-genomicranges (>= 1.18.0) + r-bioc-genomicranges (>= 1.18.0), + r-bioc-biocparallel Recommends: r-bioc-shortread Description: GNU R binary alignment (BAM), variant call (BCF), or tabix file import This package provides an interface to the 'samtools', 'bcftools', and Added: trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides =================================================================== --- trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides (rev 0) +++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/lintian-overrides 2015-10-31 18:28:47 UTC (rev 20365) @@ -0,0 +1,2 @@ +# Same file as in source tarball is installed in binary - this does not affect reproducible builds +r-bioc-rsamtools: package-contains-timestamped-gzip usr/lib/R/site-library/Rsamtools/unitTests/cases/ex1.sam.gz Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch =================================================================== --- trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch 2015-10-31 08:12:02 UTC (rev 20364) +++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/patches/use_debian_packaged_zlib.patch 2015-10-31 18:28:47 UTC (rev 20365) @@ -6,11 +6,11 @@ --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,7 +17,7 @@ LazyLoad: yes - Depends: methods, S4Vectors (>= 0.5.11), IRanges (>= 1.99.17), - GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.17.19), XVector - (>= 0.5.3), Biostrings (>= 2.33.11) --Imports: utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops -+Imports: utils, BiocGenerics (>= 0.1.3), bitops + Depends: methods, S4Vectors (>= 0.7.11), IRanges (>= 2.3.7), + GenomeInfoDb (>= 1.1.3), GenomicRanges (>= 1.21.6), XVector (>= + 0.9.1), Biostrings (>= 2.37.1) +-Imports: utils, BiocGenerics (>= 0.1.3), zlibbioc, bitops, BiocParallel ++Imports: utils, BiocGenerics (>= 0.1.3), bitops, BiocParallel Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, Modified: trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch =================================================================== --- trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch 2015-10-31 08:12:02 UTC (rev 20364) +++ trunk/packages/R/r-bioc-rsamtools/trunk/debian/watch 2015-10-31 18:28:47 UTC (rev 20365) @@ -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/Rsamtools.html .*/Rsamtools_([\d\.]+)\.tar\.gz _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
