[med-svn] r18366 - in trunk/packages/R/r-bioc-variantannotation/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Tue Oct 21 04:59:52 UTC 2014
Author: tille
Date: 2014-10-21 04:59:51 +0000 (Tue, 21 Oct 2014)
New Revision: 18366
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 upstrem version with adapted dependencies
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog 2014-10-21 04:54:05 UTC (rev 18365)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog 2014-10-21 04:59:51 UTC (rev 18366)
@@ -1,3 +1,11 @@
+r-bioc-variantannotation (1.12.0-1) UNRELEASED; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+ * Adapted dependencies
+
+ -- Andreas Tille <tille at debian.org> Tue, 21 Oct 2014 06:32:37 +0200
+
r-bioc-variantannotation (1.10.5-1) 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 2014-10-21 04:54:05 UTC (rev 18365)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2014-10-21 04:59:51 UTC (rev 18366)
@@ -2,18 +2,14 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Section: gnu-r
-Priority: optional
Testsuite: autopkgtest
+Priority: optional
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
- r-bioc-biocgenerics,
- r-bioc-genomicranges,
- r-bioc-rsamtools (>= 1.15.5),
- r-bioc-iranges,
- r-bioc-annotationdbi,
- r-bioc-genomicfeatures (>= 1.15.15)
-Standards-Version: 3.9.5
+ r-bioc-rsamtools (>= 1.18.0),
+ r-bioc-rtracklayer (>= 1.26.0)
+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/
Homepage: http://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html
@@ -23,12 +19,8 @@
Depends: ${R:Depends},
${misc:Depends},
${shlibs:Depends},
- r-bioc-biocgenerics,
- r-bioc-genomicranges,
- r-bioc-rsamtools (>= 1.15.5),
- r-bioc-iranges,
- r-bioc-annotationdbi,
- r-bioc-genomicfeatures (>= 1.15.15)
+ r-bioc-rsamtools (>= 1.18.0),
+ r-bioc-rtracklayer (>= 1.26.0)
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 2014-10-21 04:54:05 UTC (rev 18365)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch 2014-10-21 04:59:51 UTC (rev 18366)
@@ -219,8 +219,7 @@
- query <- GRanges("chr1", IRanges(start=c(1, 10, 20), width=1))
- alt <- DNAStringSet(c("G", "T", "A"))
- current <- fun(query, cdsbytx, Hsapiens, alt)
-- expected <- GRanges()
-- checkIdentical(current, expected)
+- checkIdentical(dim(mcols(current)), c(0L, 8L))
-}
-
-test_predictCoding_varAllele <- function()
@@ -250,11 +249,12 @@
-
-test_refLocsToLocalLocs <- function()
-{
+- quiet <- suppressWarnings
- ## both in 'first' cds
- query <- GRanges(seqnames="chr1",
- ranges=IRanges(rep(c(10002, 10005), 2), width=1),
- strand=c("+", "+", "-", "-"))
-- current <- refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)])
+- current <- quiet(refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)]))
- expected <- IRanges(c(2, 5, 9, 6), width=1)
- checkIdentical(values(current)[["CDSLOC"]], expected)
- expected <- c(1L, 2L, 3L, 2L)
@@ -264,7 +264,7 @@
- query <- GRanges(seqnames="chr1",
- ranges=IRanges(rep(c(10002, 10011), 2), width=1),
- strand=c("+", "+", "-", "-"))
-- current <- refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)])
+- current <- quiet(refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)]))
- expected <- IRanges(c(2, 7, 9, 4), width=1)
- checkIdentical(values(current)[["CDSLOC"]], expected)
- expected <- c(1L, 3L, 3L, 2L)
@@ -274,7 +274,7 @@
- query <- GRanges(seqnames="chr1",
- ranges=IRanges(rep(c(10010, 10013), 2), width=1),
- strand=c("+", "+", "-", "-"))
-- current <- refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)])
+- current <- quiet(refLocsToLocalLocs(query, cdsbytx=cdsbytx[c(1,3)]))
- expected <- IRanges(c(6, 9, 5, 2), width=1)
- checkIdentical(values(current)[["CDSLOC"]], expected)
- expected <- c(2L, 3L, 2L, 1L)
@@ -292,7 +292,7 @@
- current <- suppressWarnings(fun(query, cdsbytx, Hsapiens, variant))
-
- expected <- c("G", "C", "C", "C", "G", "G", "T", "A", "C")
-- checkIdentical(as.character(values(current)[["varAllele"]]), expected)
+- checkIdentical(as.character(mcols(current)$varAllele), expected)
-
- ## ignore.strand
- strand(query) <- "+"
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 2014-10-21 04:54:05 UTC (rev 18365)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch 2014-10-21 04:59:51 UTC (rev 18366)
@@ -5,20 +5,20 @@
--- a/DESCRIPTION
+++ b/DESCRIPTION
-@@ -11,7 +11,7 @@ License: Artistic-2.0
- Depends: R (>= 2.8.0), methods, BiocGenerics (>= 0.7.7), GenomicRanges
- (>= 1.13.51), Rsamtools (>= 1.15.5)
- Imports: IRanges (>= 1.21.43), XVector, Biostrings (>= 2.31.19),
-- Biobase, AnnotationDbi (>= 1.17.11), zlibbioc, BSgenome,
-+ Biobase, AnnotationDbi (>= 1.17.11), BSgenome,
- GenomicFeatures (>= 1.15.15), DBI, utils, rtracklayer
- Suggests: RUnit, BSgenome.Hsapiens.UCSC.hg19,
- TxDb.Hsapiens.UCSC.hg19.knownGene,
+@@ -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 (>= 1.17.40), Rsamtools (>= 1.17.26)
+-Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.2.3), IRanges
++Imports: utils, DBI, Biobase, S4Vectors (>= 0.2.3), IRanges
+ (>= 1.99.28), XVector (>= 0.5.6), Biostrings (>= 2.33.5),
+ AnnotationDbi (>= 1.27.9), BSgenome, rtracklayer (>= 1.25.16),
+ GenomicFeatures (>= 1.17.13)
--- a/NAMESPACE
+++ b/NAMESPACE
-@@ -8,8 +8,6 @@ import(Rsamtools)
+@@ -12,8 +12,6 @@ import(GenomicRanges)
- import(GenomicRanges)
+ import(Rsamtools)
-import(zlibbioc)
-
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