[med-svn] r20412 - in trunk/packages/R/r-bioc-variantannotation/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Fri Nov 6 12:49:15 UTC 2015
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 <tille at debian.org> 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 at 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)
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