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 <[email protected]> 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 <[email protected]> +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@signature) +- checkIdentical(formals([email protected]), formals([email protected])) +- } +- +- .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([email protected]), formals([email protected])) +- } +-} +- +-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 <[email protected]> -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() _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
