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 <[email protected]> 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 <[email protected]> -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() _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
