[med-svn] r17508 - in trunk/packages/R/r-bioc-variantannotation/trunk/debian: . patches tests
Andreas Tille
tille at moszumanska.debian.org
Thu Jul 24 07:34:32 UTC 2014
Author: tille
Date: 2014-07-24 07:34:32 +0000 (Thu, 24 Jul 2014)
New Revision: 17508
Added:
trunk/packages/R/r-bioc-variantannotation/trunk/debian/README.test
trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch
trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/
trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/control
trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/run-unit-test
Modified:
trunk/packages/R/r-bioc-variantannotation/trunk/debian/control
trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/series
Log:
Add autopkgtests and patches for tests we can not run in theses tests because of missing data packages
Added: trunk/packages/R/r-bioc-variantannotation/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/README.test (rev 0)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/README.test 2014-07-24 07:34:32 UTC (rev 17508)
@@ -0,0 +1,33 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+LC_ALL=C R --no-save <<EOT
+require("VariantAnnotation") || stop("unable to load VariantAnnotation package")
+VariantAnnotation:::.test()
+EOT
+
+in order to confirm its integrity.
+
+To successfully run this test you need some BioConductor databases as
+preconditions. Since these are not packaged for Debian the according
+tests are removed from the test suite of this package.
+
+If you want to install the as Debian packages you can use:
+
+ svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-txdb.hsapiens.ucsc.hg19.knowngene/trunk/
+
+Further databases
+
+ http://bioconductor.org/packages/release/data/annotation/html/SIFT.Hsapiens.dbSNP132.html
+ http://bioconductor.org/packages/release/data/annotation/html/PolyPhen.Hsapiens.dbSNP131.html
+ http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.UCSC.hg19.html
+
+will be needed as well but these are not yet packaged.
+
+Finally you would need to re-activate the according tests by moving the
+original files from inst/unitTests to the installation directory or you
+rebuild this package by deactivating the patch in the series file.
+
+ -- Andreas Tille <tille at debian.org> Thu, 24 Jul 2014 08:35:54 +0200
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2014-07-24 07:10:37 UTC (rev 17507)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/control 2014-07-24 07:34:32 UTC (rev 17508)
@@ -3,6 +3,7 @@
Uploaders: Andreas Tille <tille at debian.org>
Section: gnu-r
Priority: optional
+Testsuite: autopkgtest
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
Added: 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 (rev 0)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/drop_tests_requiring_large_data_sets.patch 2014-07-24 07:34:32 UTC (rev 17508)
@@ -0,0 +1,201 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 24 Jul 2014 08:35:54 +0200
+Description: Make test independent from TxDb.Hsapiens.UCSC.hg19.knownGene
+ (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
+@@ -1,132 +0,0 @@
+-library(TxDb.Hsapiens.UCSC.hg19.knownGene)
+-txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
+-cdsbytx <- cdsBy(txdb)
+-intbytx <- intronsByTranscript(txdb)
+-txbygene <- transcriptsBy(txdb, "gene")
+-
+-gr <- GRanges("chr22",
+- IRanges(c(16268137, 16287254, 16190792, 16164570,
+- 18209442, 18121652, 24314750, 25508661),
+- width=c(1,1,1,1,3,3,2,2)),
+- strand=c("-", "-", "-", "+", "+", "+", "+", "+"))
+-
+-test_locateVariants_subject <- function()
+-{
+- cols <- c("LOCATION", "QUERYID", "TXID", "CDSID")
+- loc1 <- locateVariants(gr, txdb, CodingVariants())
+- loc2 <- locateVariants(gr, cdsbytx, CodingVariants())
+- checkIdentical(mcols(loc1)[ ,cols], mcols(loc2)[ ,cols])
+-
+- loc1 <- locateVariants(gr, txdb, IntronVariants())
+- loc2 <- locateVariants(gr, intbytx, IntronVariants())
+- checkIdentical(mcols(loc1)[ ,cols], mcols(loc2)[ ,cols])
+-
+- loc1 <- locateVariants(gr, txdb, SpliceSiteVariants())
+- loc2 <- locateVariants(gr, intbytx, SpliceSiteVariants())
+- checkIdentical(mcols(loc1)[ ,cols], mcols(loc2)[ ,cols])
+-
+- loc1 <- locateVariants(gr, txdb, IntergenicVariants())
+- loc2 <- locateVariants(gr, txbygene, IntergenicVariants())
+- checkIdentical(mcols(loc1)[ ,cols], mcols(loc2)[ ,cols])
+-}
+-
+-test_locateVariants_upstream_downstream <- function()
+-{
+- loc <- locateVariants(gr, txdb, IntergenicVariants(1, 1))
+- target <- CharacterList(character(), character())
+- checkIdentical(loc$FOLLOWID, target)
+-
+- loc <- locateVariants(gr, txbygene, IntergenicVariants(2, 2))
+- target <- CharacterList(character(), "100037417")
+- checkIdentical(loc$FOLLOWID, target)
+-
+- loc <- locateVariants(gr, txbygene, IntergenicVariants(100000, 100000))
+- target <- CharacterList("23784", c("100037417","4282", "66035"))
+- checkIdentical(loc$FOLLOWID, target)
+- target <- CharacterList(character(), c("23523", "2953", "391322"))
+- checkIdentical(loc$PRECEDEID, target)
+-}
+-
+-test_locateVariants_queryAsVCF <- function()
+-{
+- fl <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
+- vcf <- readVcf(fl, "hg19")
+- vcf <- renameSeqlevels(vcf, c("1" = "chr1"))
+- loc1 <- locateVariants(vcf, txdb, IntergenicVariants())
+- loc2 <- locateVariants(rowData(vcf), txdb, IntergenicVariants())
+- checkIdentical(loc1, loc2)
+-}
+-
+-test_locateVariants_ignore.strand <- function()
+-{
+- gr <- GRanges("chr1", IRanges(c(12190, 12595, 13403), width=1), "-")
+- loc1 <- locateVariants(gr, cdsbytx, CodingVariants(),
+- ignore.strand=TRUE)
+- checkIdentical(c(1L, 2L, 3L), mcols(loc1)$QUERYID)
+- loc2 <- locateVariants(gr, cdsbytx, CodingVariants(),
+- ignore.strand=FALSE)
+- checkIdentical(integer(), mcols(loc2)$QUERYID)
+- loc1 <- locateVariants(gr, cdsbytx, SpliceSiteVariants(),
+- ignore.strand=TRUE)
+- checkIdentical(c(1L, 2L, 3L), mcols(loc1)$QUERYID)
+- loc2 <- locateVariants(gr, cdsbytx, SpliceSiteVariants(),
+- ignore.strand=FALSE)
+- checkIdentical(integer(), mcols(loc2)$QUERYID)
+-}
+-
+-test_locateVariants_asHits <- function()
+-{
+- gr <- GRanges("chr1", IRanges(c(12190, 69091, 13403), width=1))
+- loc <- locateVariants(gr, cdsbytx, CodingVariants())
+- hit <- locateVariants(gr, cdsbytx, CodingVariants(), asHits=TRUE)
+- ## annotation element
+- loc_nms <- as.character(mcols(loc)$TXID)
+- hit_nms <- names(cdsbytx[subjectHits(hit)])
+- checkIdentical(loc_nms, hit_nms)
+-
+- ## Hits lengths
+- checkIdentical(length(gr), queryLength(hit))
+- checkIdentical(length(cdsbytx), subjectLength(hit))
+-}
+-
+-.extract <- function(x, col) as.vector(mcols(x)[[col]])
+-test_locateVariants_PromoterVariants <- function()
+-{
+- s <- GRangesList(GRanges("chr1", IRanges(10, width=11), "+"),
+- GRanges("chr1", IRanges(30, width=11) , "+"))
+- ## empty
+- q <- GRanges("chr1", IRanges(15, width=1), "+")
+- current <- locateVariants(q, s, PromoterVariants(5, 5))
+- checkTrue(length(current) == 0)
+-
+- ## endpoint
+- q <- GRanges("chr1", IRanges(20, width=1), "+")
+- current <- locateVariants(q, s, PromoterVariants(5, 5))
+- checkTrue(length(current) == 0)
+-
+- ## strand
+- q <- GRanges(c("chr1", "chr1"), IRanges(c(8, 12), width=1), "+")
+- current <- locateVariants(q, s, PromoterVariants(5, 5))
+- checkEquals(c(1L, 2L), .extract(current, "QUERYID"))
+- strand(s) <- RleList(Rle(factor("*")), Rle(factor("*")))
+- strand(q) <- "*"
+- current <- suppressWarnings(locateVariants(q, s, PromoterVariants(5, 5)))
+- checkEquals(c(1L, 2L), .extract(current, "QUERYID"))
+- q <- GRanges(c("chr1", "chr1"), IRanges(c(21, 41), width=1), "-")
+- strand(s) <- RleList(Rle(factor("-")), Rle(factor("-")))
+- current <- locateVariants(q, s, PromoterVariants(5, 5))
+- checkEquals(c(1L, 2L), .extract(current, "QUERYID"))
+-
+- q <- GRanges(c("chr2", "chr2"), IRanges(c(9, 10), width=1), "+")
+- s <- GRangesList(GRanges("chr2", IRanges(10, width=11), "+"))
+- current <- locateVariants(q, s, PromoterVariants(5, 0))
+- checkEquals(1L, .extract(current, "QUERYID"))
+- current <- locateVariants(q, s, PromoterVariants(5, 1))
+- checkEquals(c(1L, 2L), .extract(current, "QUERYID"))
+- current <- locateVariants(q, s, PromoterVariants(0, 0))
+- checkTrue(length(current) == 0L)
+-
+- q <- GRanges("chr22", IRanges(50310410, 50310420))
+- current <- locateVariants(q, txdb, PromoterVariants())
+- checkIdentical(unique(current$GENEID), "79174")
+-}
Modified: trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/series 2014-07-24 07:10:37 UTC (rev 17507)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/patches/series 2014-07-24 07:34:32 UTC (rev 17508)
@@ -1 +1,2 @@
use_debian_packaged_zlib.patch
+drop_tests_requiring_large_data_sets.patch
Added: trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/control
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/control (rev 0)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/control 2014-07-24 07:34:32 UTC (rev 17508)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, r-cran-runit
+Restrictions: allow-stderr
Added: trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/run-unit-test (rev 0)
+++ trunk/packages/R/r-bioc-variantannotation/trunk/debian/tests/run-unit-test 2014-07-24 07:34:32 UTC (rev 17508)
@@ -0,0 +1,7 @@
+#!/bin/sh -e
+
+LC_ALL=C R --no-save <<EOT
+require("VariantAnnotation")
+VariantAnnotation:::.test()
+EOT
+
More information about the debian-med-commit
mailing list