Author: tille Date: 2015-11-06 12:49:14 +0000 (Fri, 06 Nov 2015) New Revision: 20412
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog trunk/packages/R/r-bioc-variantannotation/trunk/debian/control trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch Log: New upstream version Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog =================================================================== --- trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog 2015-11-06 12:06:43 UTC (rev 20411) +++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog 2015-11-06 12:49:14 UTC (rev 20412) @@ -1,3 +1,10 @@ +r-bioc-variantannotation (1.16.3-1) unstable; urgency=medium + + * New upstream version + Closes: #804223 + + -- Andreas Tille <[email protected]> Fri, 06 Nov 2015 13:08:13 +0100 + r-bioc-variantannotation (1.14.13-1) unstable; urgency=medium * New upstream version Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/control =================================================================== --- trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2015-11-06 12:06:43 UTC (rev 20411) +++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2015-11-06 12:49:14 UTC (rev 20412) @@ -6,8 +6,8 @@ Build-Depends: debhelper (>= 9), cdbs, r-base-dev, - r-bioc-genomicfeatures (>= 1.20.1), - r-bioc-bsgenome (>= 1.36.1) + r-bioc-genomicfeatures (>= 1.22.1), + r-bioc-bsgenome (>= 1.38.0) Standards-Version: 3.9.6 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-variantannotation/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-variantannotation/trunk/ @@ -18,8 +18,8 @@ Depends: ${R:Depends}, ${misc:Depends}, ${shlibs:Depends}, - r-bioc-genomicfeatures (>= 1.18.0), - r-bioc-bsgenome (>= 1.34.0) + r-bioc-genomicfeatures (>= 1.22.0), + r-bioc-bsgenome (>= 1.38.0) Suggests: r-bioc-snpstats Description: BioConductor annotation of genetic variants This BioConductor package provides R functions to annotate variants, Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch =================================================================== --- trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch 2015-11-06 12:06:43 UTC (rev 20411) +++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch 2015-11-06 12:49:14 UTC (rev 20412) @@ -3,67 +3,6 @@ Description: Make test independent from TxDb.Hsapiens.UCSC.hg19.knownGene and other not packaged databases (see debian/README.test) ---- a/inst/unitTests/test_SIFTandPolyPhen.R -+++ /dev/null -@@ -1,58 +0,0 @@ --library(SIFT.Hsapiens.dbSNP132) --#library(SIFT.Hsapiens.dbSNP137) --library(PolyPhen.Hsapiens.dbSNP131) --quiet <- suppressWarnings -- --test_SIFT_132 <- function() --{ -- db <- SIFT.Hsapiens.dbSNP132 -- scol <- columns(db) -- checkIdentical(length(scol), 10L) -- -- res <- select(db, "rs2142947") -- checkIdentical(nrow(res), 4L) -- -- res <- select(db, "rs2142947", columns="AACHANGE") -- checkIdentical(nrow(res), 1L) -- -- res <- -- quiet(select(db, keys=c("rs17970171", "INVALID", "rs17970171"))) -- checkIdentical(nrow(res), 9L) -- checkTrue(all(res$RSID %in% c("rs17970171", "INVALID"))) --} -- --#test_SIFT_137 <- function() --#{ --# db <- SIFT.Hsapiens.dbSNP137 --# scol <- columns(db) --# checkIdentical(length(scol), 18L) --# --# res <- select(db, keys=keys(db)[20:21]) --# checkIdentical(nrow(res), 3L) --# checkIdentical(res$DBSNPID, c(665L, 665L, 666L)) --# --# res <- quiet(select(db, keys=c("665", "foo", "666"))) --# checkIdentical(res$DBSNPID, c("665", "665", "foo", "666")) --# --# res <- quiet(select(db, keys=c(665, 666), columns=c("LENGTH", "foo"))) --# checkIdentical(res, data.frame()) --#} -- --test_PolyPhen <- function() --{ -- db <- PolyPhen.Hsapiens.dbSNP131 -- pcol <- columns(db) -- checkIdentical(length(pcol), 58L) -- -- res <- select(db, "rs3026284") -- checkIdentical(nrow(res), 2L) -- -- res <- select(db, "rs3026284", columns="POS") -- checkIdentical(nrow(res), 1L) -- -- res <- -- suppressWarnings(select(db, keys=c("rs3026284", "INVALID", "rs3026284"))) -- checkIdentical(nrow(res), 5L) -- checkTrue(all(res$RSID %in% c("rs3026284", "INVALID"))) --} -- --- a/inst/unitTests/test_locateVariants-methods.R +++ /dev/null @@ -1,136 +0,0 @@ @@ -317,3 +256,45 @@ - checkIdentical(mcols(current)$CDSLOC, IRanges(3, 3)) -} - +--- a/inst/unitTests/test_SIFTandPolyPhen.R ++++ /dev/null +@@ -1,39 +0,0 @@ +-library(SIFT.Hsapiens.dbSNP132) +-library(PolyPhen.Hsapiens.dbSNP131) +-quiet <- suppressWarnings +- +-test_SIFT_132 <- function() +-{ +- db <- SIFT.Hsapiens.dbSNP132 +- scol <- columns(db) +- checkIdentical(length(scol), 10L) +- +- res <- select(db, "rs2142947") +- checkIdentical(nrow(res), 4L) +- +- res <- select(db, "rs2142947", columns="AACHANGE") +- checkIdentical(nrow(res), 1L) +- +- res <- +- quiet(select(db, keys=c("rs17970171", "INVALID", "rs17970171"))) +- checkIdentical(nrow(res), 9L) +- checkTrue(all(res$RSID %in% c("rs17970171", "INVALID"))) +-} +- +-test_PolyPhen <- function() +-{ +- db <- PolyPhen.Hsapiens.dbSNP131 +- pcol <- columns(db) +- checkIdentical(length(pcol), 58L) +- +- res <- select(db, "rs3026284") +- checkIdentical(nrow(res), 2L) +- +- res <- select(db, "rs3026284", columns="POS") +- checkIdentical(nrow(res), 1L) +- +- res <- +- suppressWarnings(select(db, keys=c("rs3026284", "INVALID", "rs3026284"))) +- checkIdentical(nrow(res), 5L) +- checkTrue(all(res$RSID %in% c("rs3026284", "INVALID"))) +-} Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch =================================================================== --- trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch 2015-11-06 12:06:43 UTC (rev 20411) +++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch 2015-11-06 12:49:14 UTC (rev 20412) @@ -3,20 +3,9 @@ Description: If the systems includes zlib natively there is no point in requiring the import of zlibbioc ---- a/DESCRIPTION -+++ b/DESCRIPTION -@@ -12,7 +12,7 @@ Authors@R: c(person("Valerie", "Obenchai - License: Artistic-2.0 - Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.7.7), GenomeInfoDb - (>= 1.1.3), GenomicRanges (>= 1.19.47), Rsamtools (>= 1.19.52) --Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.5.14), IRanges -+Imports: utils, DBI, Biobase, S4Vectors (>= 0.5.14), IRanges - (>= 2.1.27), XVector (>= 0.5.6), Biostrings (>= 2.33.5), - AnnotationDbi (>= 1.27.9), BSgenome, rtracklayer (>= 1.25.16), - GenomicFeatures (>= 1.19.17) --- a/NAMESPACE +++ b/NAMESPACE -@@ -12,8 +12,6 @@ import(GenomicRanges) +@@ -16,8 +16,6 @@ import(SummarizedExperiment) import(Rsamtools) @@ -25,3 +14,14 @@ importClassesFrom(Biobase, AssayData ) +--- a/DESCRIPTION ++++ b/DESCRIPTION +@@ -13,7 +13,7 @@ License: Artistic-2.0 + Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.15.3), GenomeInfoDb + (>= 1.1.3), GenomicRanges (>= 1.19.47), SummarizedExperiment + (>= 0.3.1), Rsamtools (>= 1.19.52) +-Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.7.11), IRanges ++Imports: utils, DBI, Biobase, S4Vectors (>= 0.7.11), IRanges + (>= 2.3.25), XVector (>= 0.5.6), Biostrings (>= 2.33.5), + AnnotationDbi (>= 1.27.9), BSgenome (>= 1.37.6), rtracklayer + (>= 1.25.16), GenomicFeatures (>= 1.19.17) _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
