[med-svn] r19204 - in trunk/packages/R/r-bioc-genomicranges/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Mon May 11 07:35:27 UTC 2015
Author: tille
Date: 2015-05-11 07:35:26 +0000 (Mon, 11 May 2015)
New Revision: 19204
Modified:
trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.test
trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog
trunk/packages/R/r-bioc-genomicranges/trunk/debian/control
trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch
Log:
New upstream version including adapting patch for test suite
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.test
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.test 2015-05-10 07:29:35 UTC (rev 19203)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/README.test 2015-05-11 07:35:26 UTC (rev 19204)
@@ -11,6 +11,8 @@
in order to confirm its integrity.
Attention: The full test suite requires the database
- TxDb.Dmelanogaster.UCSC.dm3.ensGene
+ http://www.bioconductor.org/packages/release/data/annotation/html/hgu95av2.db.html
which is not packaged for Debian. The according test was dropped
from the test suite to run it successfully on a plain Debian machine.
+If you might want to test against this database you need to deactivate
+the patch in debian/patches/series and rebuild the package.
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog 2015-05-10 07:29:35 UTC (rev 19203)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog 2015-05-11 07:35:26 UTC (rev 19204)
@@ -1,3 +1,9 @@
+r-bioc-genomicranges (1.20.3-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Andreas Tille <tille at debian.org> Sun, 10 May 2015 00:33:03 +0200
+
r-bioc-genomicranges (1.18.1-1) experimental; urgency=medium
* New upstream version
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/control 2015-05-10 07:29:35 UTC (rev 19203)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/control 2015-05-11 07:35:26 UTC (rev 19204)
@@ -7,7 +7,7 @@
Build-Depends: debhelper (>= 9),
cdbs,
r-base-dev,
- r-bioc-genomeinfodb (>= 1.2.0),
+ r-bioc-genomeinfodb (>= 1.4.0),
r-bioc-xvector (>= 0.6.0)
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch 2015-05-10 07:29:35 UTC (rev 19203)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch 2015-05-11 07:35:26 UTC (rev 19204)
@@ -1,92 +1,44 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sat, 18 Oct 2014 08:07:45 +0200
+Last-Update: Sun, 10 May 2015 00:33:03 +0200
Description: The full test suite requires the database
- TxDb.Dmelanogaster.UCSC.dm3.ensGene
- which is not packaged for Debian. The according test was dropped
- from the test suite to run it successfully on a plain Debian machine.
+ http://www.bioconductor.org/packages/release/data/annotation/html/hgu95av2.db.html
+
+ Whithout this patch (=including the tests below) The unit tests will end in:
+
+ ERROR in test_GenomicRanges_SummarizedExperiment_coercion_mappingFunctions: Error : Failed to load 'hgu95av2.db' package
+ Test files with failing tests
---- a/inst/unitTests/test_mapCoords-methods.R
-+++ /dev/null
-@@ -1,81 +0,0 @@
--library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
--txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
--cdsbytx <- cdsBy(txdb, "tx")[1:3]
+ test_SummarizedExperiment-class.R
+ test_GenomicRanges_SummarizedExperiment_coercion_mappingFunctions
+
+
+--- a/inst/unitTests/test_SummarizedExperiment-class.R
++++ b/inst/unitTests/test_SummarizedExperiment-class.R
+@@ -501,26 +501,6 @@ test_GenomicRanges_SummarizedExperiment_
+ makeSummarizedExperimentFromExpressionSet(ExpressionSet(),
+ probeRangeMapper)))
+
+- ## valid object from sample ExpressionSet
+- se1 <- makeSummarizedExperimentFromExpressionSet(eset1, probeRangeMapper)
+- checkTrue(validObject(se1))
-
--test_mapCoords_output <- function()
--{
-- cds <- cdsbytx
-- from <- GRanges("chr2L", IRanges(c(7500, 8400, 9000),
-- width = 200, names = LETTERS[1:3]))
-- x <- mapCoords(from, cds)
-- checkTrue(length(x) == 3L)
-- checkIdentical(names(x), c("B", "B", "C"))
-- checkIdentical(names(mcols(x)), c("queryHits", "subjectHits"))
-- checkTrue(all(width(x) == 200L))
+- ## Granges returned have rownames that were from the featureNames
+- checkTrue(all(rownames(rowRanges(se1)) %in% Biobase::featureNames(eset1)))
-
-- x <- mapCoords(from, cds, elt.hits=TRUE)
-- checkTrue("eltHits" %in% names(mcols(x)))
+- ## geneRangeMapper
+- ## valid object from empty object
+- checkTrue(validObject(
+- makeSummarizedExperimentFromExpressionSet(ExpressionSet(),
+- geneRangeMapper(NULL))))
-
-- x <- mapCoords(from, cds, elt.loc=TRUE)
-- checkTrue("eltLoc" %in% names(mcols(x)))
--}
+- ## valid object from sample ExpressionSet
+- se2 <- makeSummarizedExperimentFromExpressionSet(eset1,
+- geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))
+- checkTrue(validObject(se2))
-
--test_mapCoords_outerlist_vs_listelt <- function()
--{
-- cds <- cdsbytx
-- from <- GRanges("chr2L", IRanges(c(7500, 8400, 9000), width = 200))
-- strand(from) <- "+"
-- x <- mapCoords(from, cds, elt.loc=TRUE)
-- checkIdentical(start(x), c(645L, 609L, 1167L))
-- checkIdentical(start(mcols(x)$eltLoc), c(208L, 172L, 333L))
--
-- from <- GRanges("chr2L", IRanges(c(8200, 9000), width = 200))
-- strand(from) <- "-"
-- strand(cds) <- "-"
-- x <- mapCoords(from, cds, elt.loc=TRUE)
-- checkIdentical(start(x), c(212L, 800L, 78L))
-- checkIdentical(start(mcols(x)$eltLoc), c(212L, 191L, 78L))
--}
--
--test_mapCoords_range_order_pos <- function()
--{
-- from <- GRanges("chrA", IRanges(43522349, width=1), strand="+")
-- ## Strand '+' smallest range first
-- grl <- GRangesList(GRanges("chrA",
-- IRanges(c(43522244, 43528406),
-- c(43524145, 43528644)), strand="+"))
-- x <- mapCoords(from, grl)
-- checkTrue(start(x) == 106L)
--
-- ## Strand '+' largest range first
-- grl <- GRangesList(GRanges("chrA",
-- IRanges(c(43528406, 43522244),
-- c(43528644, 43524145)), strand="+"))
-- x <- mapCoords(from, grl)
-- checkTrue(start(x) == 106L)
--}
--
--test_mapCoords_range_order_neg <- function()
--{
-- from <- GRanges("chrA", IRanges(43522349, width=1), strand="-")
--
-- ## Strand '-' smallest range first
-- grl <- GRangesList(GRanges("chrA",
-- IRanges(c(43522244, 43528406),
-- c(43524145, 43528644)), strand="-"))
-- x <- mapCoords(from, grl, elt.loc = TRUE)
-- checkTrue(start(x) == 2036L)
-- checkTrue(start(mcols(x)$eltLoc) == 1797L)
--
-- ## Strand '-' largest range first
-- grl <- GRangesList(GRanges("chrA",
-- IRanges(c(43528406, 43522244),
-- c(43528644, 43524145)), strand="-"))
-- x <- mapCoords(from, grl, elt.loc = TRUE)
-- checkTrue(start(x) == 2036L)
-- checkTrue(start(mcols(x)$eltLoc) == 1797L)
--
-- ## ignore.strand
-- x <- mapCoords(from, grl, ignore.strand=TRUE)
-- checkTrue(all(start(x) == 106L))
--}
+- ## Granges returned have rownames that were from the featureNames
+- checkTrue(all(rownames(rowRanges(se2)) %in% Biobase::featureNames(eset1)))
+ }
+
+ test_SummarizedExperiment_assays_4d <- function()
More information about the debian-med-commit
mailing list