[med-svn] r20343 - in trunk/packages/R/r-bioc-genomicranges/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Fri Oct 30 12:55:31 UTC 2015
Author: tille
Date: 2015-10-30 12:55:30 +0000 (Fri, 30 Oct 2015)
New Revision: 20343
Added:
trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/ignore_test_requiring_SummarizedExperiment.patch
Removed:
trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch
Modified:
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/series
Log:
New upstream version, Skip test requiring extra module SummarizedExperiment
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog 2015-10-30 12:07:30 UTC (rev 20342)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/changelog 2015-10-30 12:55:30 UTC (rev 20343)
@@ -1,3 +1,10 @@
+r-bioc-genomicranges (1.22.0-1) unstable; urgency=medium
+
+ * New upstream version
+ * Skip test requiring extra module SummarizedExperiment
+
+ -- Andreas Tille <tille at debian.org> Fri, 30 Oct 2015 08:55:15 +0100
+
r-bioc-genomicranges (1.20.8-1) unstable; urgency=medium
* New upstream version
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/control
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/control 2015-10-30 12:07:30 UTC (rev 20342)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/control 2015-10-30 12:55:30 UTC (rev 20343)
@@ -8,7 +8,7 @@
cdbs,
r-base-dev,
r-bioc-genomeinfodb (>= 1.4.0),
- r-bioc-xvector (>= 0.6.0)
+ r-bioc-xvector (>= 0.10.0)
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-bioc-genomicranges/trunk/
@@ -19,8 +19,8 @@
Depends: ${R:Depends},
${shlibs:Depends},
${misc:Depends},
- r-bioc-genomeinfodb (>= 1.2.0),
- r-bioc-xvector (>= 0.6.0)
+ r-bioc-genomeinfodb (>= 1.4.0),
+ r-bioc-xvector (>= 0.10.0)
Recommends: r-cran-digest
Description: BioConductor representation and manipulation of genomic intervals
The ability to efficiently store genomic annotations and alignments is
Added: trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/ignore_test_requiring_SummarizedExperiment.patch
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/ignore_test_requiring_SummarizedExperiment.patch (rev 0)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/ignore_test_requiring_SummarizedExperiment.patch 2015-10-30 12:55:30 UTC (rev 20343)
@@ -0,0 +1,140 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 30 Oct 2015 08:55:15 +0100
+Description: Skip test requiring extra module SummarizedExperiment
+ https://www.bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html
+
+--- a/inst/unitTests/test_SummarizedExperiment-rowData-methods.R
++++ b/inst/unitTests/test_SummarizedExperiment-rowData-methods.R
+@@ -1,130 +1,2 @@
+-library(digest)
+-
+-.singleDispatch <-
+- c("coverage", "disjointBins", "duplicated", "end", "end<-",
+- "flank", "granges", "isDisjoint", "narrow", "ranges",
+- "resize", "restrict", "seqinfo", "seqnames", "shift",
+- "start", "start<-", "strand", "width", "width<-",
+- "strand", "ranges", "seqinfo<-")
+-
+-.twoDispatch <- c("nearest", "precede", "follow", "distance",
+- "distanceToNearest",
+- ## FIXME: "findOverlaps", "countOverlaps",
+- "subsetByOverlaps")
+-
+-.otherFuns <- c("order", "rank", "sort")
+-
+-m <- matrix(1, 5, 3, dimnames=list(NULL, NULL))
+-mlst <- matrix(1, 3, 3, dimnames=list(NULL, NULL))
+-mList <- list(m, mlst)
+-assaysList <- list(gr=SimpleList(m=m), grl=SimpleList(m=mlst))
+-rowRangesList <-
+- list(gr=GRanges("chr1", IRanges(1:5, 10)),
+- grl=split(GRanges("chr1", IRanges(1:5, 10)), c(1,1,2,2,3)))
+-names(rowRangesList[["grl"]]) <- NULL
+-colData <- DataFrame(x=letters[1:3])
+-
+-## a list of one SE with GRanges and one with GRangesList
+-ssetList <-
+- list(SummarizedExperiment(
+- assays=assaysList[["gr"]],
+- rowRanges=rowRangesList[["gr"]],
+- colData=colData),
+- SummarizedExperiment(
+- assays=assaysList[["grl"]],
+- rowRanges=rowRangesList[["grl"]],
+- colData=colData))
+-
+-test_SummarizedExperiment_GRanges_API <- function() {
+- ## are we targetting the correct API? signature for
+- ## SummarizedExperiment method should match signature for
+- ## GenomicRanges or similar, as in each test below
+-
+- for (.fun in .singleDispatch) {
+- generic <- getGeneric(.fun)
+- method <- getMethod(.fun, "SummarizedExperiment")
+- checkIdentical("x", generic at signature)
+- checkIdentical(formals(generic at .Data), formals(method at .Data))
+- }
+-
+- .sig <- c("SummarizedExperiment", "SummarizedExperiment")
+- .targ <- c("GenomicRanges", "GenomicRanges")
+- for (.fun in .twoDispatch) {
+- .siglocal <- body(getMethod(.fun, .sig)@.Data)[[2]][[3]]
+- .targlocal <- body(getMethod(.fun, .targ)@.Data)[[2]][[3]]
+- checkIdentical(formals(.targlocal), formals(.siglocal))
+- }
+-
+- ## FIXME: compare, Compare
+-
+- .sig <- "SummarizedExperiment"
+- for (.fun in .otherFuns) {
+- generic <- getGeneric(.fun)
+- method <- getMethod(.fun, "SummarizedExperiment")
+- checkIdentical(formals(generic at .Data), formals(method at .Data))
+- }
+-}
+-
+-test_SummarizedExperiment_GRanges_values <- function()
+-{
+- x <- ssetList[[1]]
+- isAssign <- grep("<-$", .singleDispatch, value=TRUE)
+- needArgs <- c("flank", "resize")
+- isEndomorphism <- c("narrow", "restrict", "shift")
+- .funs <- setdiff(.singleDispatch,
+- c(isAssign, needArgs, isEndomorphism))
+- ## 'exp' created after manual inspection of results
+- exp <- setNames(c("1f7c0", "35e2c", "02dde", "80339", "49a3f",
+- "72f53", "86757", "77198", "ec53a", "35e2c",
+- "625d9", "3c90a"), .funs)
+- obs <- sapply(.funs, function(.fun) {
+- substr(digest(getGeneric(.fun)(x)), 1, 5)
+- })
+- checkIdentical(exp, obs)
+-
+- .funs <- isAssign
+- .gets <- sub("<-$", "", isAssign)
+- for (i in seq_along(isAssign)) {
+- ## self-assignment isomorphism
+- value <- getGeneric(.gets[[i]])(x)
+- x1 <- do.call(isAssign[[i]], list(x, value=value))
+- checkIdentical(x, x1)
+- }
+-
+- for (.fun in needArgs) {
+- ## all needArgs operate on rowRanges
+- generic <- getGeneric(.fun)
+- x1 <- x; rowRanges(x1) <- generic(rowRanges(x1), 5)
+- checkIdentical(x1, generic(x, 5))
+- }
+- ## isEndomorphism
+- for (.fun in isEndomorphism) {
+- generic <- getGeneric(.fun)
+- obs <- generic(x)
+- checkIdentical(generic(rowRanges(x)), rowRanges(obs))
+- checkIdentical(assays(x), assays(obs))
+- }
+-
+- .funs <- c(.twoDispatch[.twoDispatch != "subsetByOverlaps"],
+- "findOverlaps", "countOverlaps")
+- x1 <- shift(x, seq_len(nrow(x)) * 5)
+- for (.fun in .funs) {
+- generic <- getGeneric(.fun)
+- exp <- generic(rowRanges(x1), rowRanges(x1))
+- obs <- generic(x1, x1)
+- checkIdentical(obs, exp)
+- }
+- # nearest,SummarizedExperiment,missing-method
+- checkIdentical(nearest(rowRanges(x1)), nearest(x1))
+- checkIdentical(subsetByOverlaps(rowRanges(x1), rowRanges(x1)[3]),
+- rowRanges(subsetByOverlaps(x1, x1[3])))
+-}
+-
+-test_SummarizedExperiment_split <- function() {
+- gr <- GRanges(Rle(c("A", "B"), c(2, 3)), IRanges(1:5, 10))
+- se <- SummarizedExperiment(m, rowRanges=gr, colData=colData)
+- ## FIXME: unname should not be necessary
+- obs <- split(se, seqnames(se))
+- exp <- SimpleList(A=se[1:2], B=se[3:5])
+- checkEquals(obs, exp)
+-}
++# The test would require packaging an additional BioConductor module
++# https://www.bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html
Modified: trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/series
===================================================================
--- trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/series 2015-10-30 12:07:30 UTC (rev 20342)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/series 2015-10-30 12:55:30 UTC (rev 20343)
@@ -1 +1 @@
-skip_test_requiring_not_packaged_db.patch
+ignore_test_requiring_SummarizedExperiment.patch
Deleted: 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 2015-10-30 12:07:30 UTC (rev 20342)
+++ trunk/packages/R/r-bioc-genomicranges/trunk/debian/patches/skip_test_requiring_not_packaged_db.patch 2015-10-30 12:55:30 UTC (rev 20343)
@@ -1,44 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 10 May 2015 00:33:03 +0200
-Description: The full test suite requires the database
- 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
-
- 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))
--
-- ## Granges returned have rownames that were from the featureNames
-- checkTrue(all(rownames(rowRanges(se1)) %in% Biobase::featureNames(eset1)))
--
-- ## geneRangeMapper
-- ## valid object from empty object
-- checkTrue(validObject(
-- makeSummarizedExperimentFromExpressionSet(ExpressionSet(),
-- geneRangeMapper(NULL))))
--
-- ## valid object from sample ExpressionSet
-- se2 <- makeSummarizedExperimentFromExpressionSet(eset1,
-- geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))
-- checkTrue(validObject(se2))
--
-- ## Granges returned have rownames that were from the featureNames
-- checkTrue(all(rownames(rowRanges(se2)) %in% Biobase::featureNames(eset1)))
- }
-
- test_SummarizedExperiment_assays_4d <- function()
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