[med-svn] r21933 - in trunk/packages/R/r-bioc-variantannotation/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Wed May 11 08:40:48 UTC 2016
Author: tille
Date: 2016-05-11 08:40:48 +0000 (Wed, 11 May 2016)
New Revision: 21933
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 2016-05-11 07:30:41 UTC (rev 21932)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/changelog 2016-05-11 08:40:48 UTC (rev 21933)
@@ -1,3 +1,10 @@
+r-bioc-variantannotation (1.18.0-1) unstable; urgency=medium
+
+ * New upstream version
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Wed, 11 May 2016 10:05:34 +0200
+
r-bioc-variantannotation (1.16.3-1) 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 2016-05-11 07:30:41 UTC (rev 21932)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2016-05-11 08:40:48 UTC (rev 21933)
@@ -8,8 +8,8 @@
r-base-dev,
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/
+Standards-Version: 3.9.8
+Vcs-Browser: https://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
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 2016-05-11 07:30:41 UTC (rev 21932)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch 2016-05-11 08:40:48 UTC (rev 21933)
@@ -139,9 +139,51 @@
- checkIdentical(loc$QUERYID, as.integer(1:7))
- checkIdentical(length(coding) , 6L)
- checkIdentical(loc$CDSID[1:6], coding$CDSID)
-- checkIdentical(as.character(coding$VARCODON[c(1,4)]),
+- checkIdentical(unname(as.character(coding$VARCODON[c(1,4)])),
- as.character(DNAStringSet(c("AAG", "TAG"))))
-}
+--- a/inst/unitTests/test_SIFTandPolyPhen.R
++++ /dev/null
+@@ -1,39 +0,0 @@
+-library(SIFT.Hsapiens.dbSNP132)
+-library(PolyPhen.Hsapiens.dbSNP131)
+-quiet <- suppressWarnings
+-
+-test_SIFT_132 <- function()
+-{
+- db <- SIFT.Hsapiens.dbSNP132
+- scol <- columns(db)
+- checkIdentical(length(scol), 10L)
+-
+- res <- select(db, "rs2142947")
+- checkIdentical(nrow(res), 4L)
+-
+- res <- select(db, "rs2142947", columns="AACHANGE")
+- checkIdentical(nrow(res), 1L)
+-
+- res <-
+- quiet(select(db, keys=c("rs17970171", "INVALID", "rs17970171")))
+- checkIdentical(nrow(res), 9L)
+- checkTrue(all(res$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$RSID %in% c("rs3026284", "INVALID")))
+-}
--- a/inst/unitTests/test_predictCoding-methods.R
+++ /dev/null
@@ -1,111 +0,0 @@
@@ -187,7 +229,7 @@
- query <- GRanges("chr1", IRanges(rep(10101, 2), width=c(2,3)),
- variant=variant)
- current <- quiet(fun(query, cdsbytx[1:2], Hsapiens, variant))
-- checkIdentical(as.character(mcols(current)$VARCODON),
+- checkIdentical(unname(as.character(mcols(current)$VARCODON)),
- c("TATCCGG", "TTCCGG"))
-}
-
@@ -256,45 +298,3 @@
- checkIdentical(mcols(current)$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 2016-05-11 07:30:41 UTC (rev 21932)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/use_debian_packaged_zlib.patch 2016-05-11 08:40:48 UTC (rev 21933)
@@ -18,10 +18,10 @@
+++ 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
+ (>= 1.7.1), GenomicRanges (>= 1.19.47), SummarizedExperiment
+ (>= 0.3.1), Rsamtools (>= 1.23.10)
+-Imports: utils, DBI, zlibbioc, Biobase, S4Vectors (>= 0.9.47), IRanges
++Imports: utils, DBI, Biobase, S4Vectors (>= 0.9.47), 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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