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Author: Michael R. Crusoe <crusoe@debian.org>
Description: skip tests that use the unpackaged optional dependency 'chihaya'
Forwarded: not-needed
--- r-bioc-alabaster.matrix.orig/tests/testthat/test-stage-array.R
+++ r-bioc-alabaster.matrix/tests/testthat/test-stage-array.R
@@ -116,117 +116,6 @@
expect_equal(as.array(arr2), as.array(y))
})
-test_that("stageObject works with DelayedArrays with preserved operations", {
- dir <- tempfile()
- odir <- file.path(dir, experiment)
- dir.create(odir, recursive=TRUE)
-
- library(DelayedArray)
- x <- DelayedArray(arr)
- x <- log2(x / runif(nrow(x)) + 1)
-
- old <- preserveDelayedOperations(TRUE)
- info <- stageObject(x, dir, file.path(experiment, assay))
- preserveDelayedOperations(old)
- expect_match(info$`$schema`, "hdf5_delayed_array")
- expect_error(alabaster.base::.writeMetadata(info, dir=dir), NA)
-
- arr2 <- loadArray(info, project=dir)
- expect_equal(unname(as.array(arr2)), unname(as.array(x)))
-})
-
-test_that("stageObject works with DelayedArrays with local references", {
- dir <- tempfile()
- odir <- file.path(dir, experiment)
- dir.create(odir, recursive=TRUE)
-
- info <- stageObject(arr, dir, paste0(experiment, "/raw"))
- alabaster.base::.writeMetadata(info, dir=dir)
- raw.path <- info$path
-
- # Adding delayed operations.
- library(DelayedArray)
- x <- DelayedArray(arr)
- x <- log2(x / runif(nrow(x)) + 1)
-
- old <- preserveDelayedOperations(TRUE)
- info <- stageObject(x, dir, file.path(experiment, assay))
- preserveDelayedOperations(old)
-
- expect_match(info$`$schema`, "hdf5_delayed_array")
- expect_error(alabaster.base::.writeMetadata(info, dir=dir), NA)
-
- # Manually replacing the seed with a local reference.
- fpath <- file.path(dir, info$path)
- rhdf5::h5delete(fpath, "data/seed/seed/seed")
- rhdf5::h5createGroup(fpath, "data/seed/seed/seed")
- rhdf5::h5write(dim(arr), fpath, "data/seed/seed/seed/dimensions")
- rhdf5::h5write("integer", fpath, "data/seed/seed/seed/type")
- rhdf5::h5write(raw.path, fpath, "data/seed/seed/seed/path")
-
- {
- fhandle = rhdf5::H5Fopen(fpath, "H5F_ACC_RDWR")
- ghandle = rhdf5::H5Gopen(fhandle, "data/seed/seed/seed")
- rhdf5::h5writeAttribute("array", ghandle, "delayed_type", asScalar=TRUE)
- rhdf5::h5writeAttribute("custom alabaster local array", ghandle, "delayed_array", asScalar=TRUE)
- rhdf5::H5Gclose(ghandle)
- rhdf5::H5Fclose(fhandle)
- }
-
- # Now seeing if we can load it.
- arr2 <- loadArray(info, project=dir)
- expect_equal(unname(as.array(arr2)), unname(as.array(x)))
-})
-
-test_that("stageObject recycles existing HDF5Arrays", {
- dir <- tempfile()
- dir.create(dir, recursive=TRUE)
-
- library(HDF5Array)
- x <- as(matrix(runif(1000), 10, 100), "HDF5Array")
- rhdf5::h5write("foo", path(x), "bar") # injecting a little something to distinguish it from a rewritten file.
-
- {
- info <- stageObject(x, dir, "dense")
- expect_false(identical(file.size(path(x)), file.size(file.path(dir, info$path)))) # negative control that triggers the fallback.
- arr2 <- loadArray(info, project=dir)
- expect_equal(unname(as.array(arr2)), unname(as.array(x)))
- }
-
- old <- recycleHdf5Files(TRUE)
- on.exit(recycleHdf5Files(old))
-
- {
- info <- stageObject(x, dir, "dense2")
- expect_match(info$`$schema`, "hdf5_dense_array")
- expect_error(alabaster.base::.writeMetadata(info, dir=dir), NA)
- expect_identical(file.size(path(x)), file.size(file.path(dir, info$path))) # same file.
-
- arr2 <- loadArray(info, project=dir)
- expect_equal(unname(as.array(arr2)), unname(as.array(x)))
- }
-
- {
- y <- Matrix::rsparsematrix(20, 50, density=0.1)
- tmp <- tempfile(fileext=".h5")
- rhdf5::h5createFile(tmp)
- rhdf5::h5createGroup(tmp, "foo")
- rhdf5::h5write(y@p, tmp, "foo/indptr")
- rhdf5::h5write(y@i, tmp, "foo/indices")
- rhdf5::h5write(y@x, tmp, "foo/data")
- rhdf5::h5write(dim(y), tmp, "foo/shape")
- x <- H5SparseMatrix(tmp, "foo")
-
- info <- stageObject(x, dir, "sparse")
- expect_match(info$`$schema`, "hdf5_sparse_matrix")
- expect_error(alabaster.base::.writeMetadata(info, dir=dir), NA)
- expect_identical(file.size(path(x)), file.size(file.path(dir, info$path)))
-
- arr2 <- loadArray(info, project=dir)
- expect_equal(unname(as.array(arr2)), unname(as.array(x)))
- }
-})
-
test_that("reading arrays work with non-default NA placeholders", {
dir <- tempfile()
dir.create(dir, recursive=TRUE)
--- r-bioc-alabaster.matrix.orig/tests/testthat/test-stage-matrix.R
+++ r-bioc-alabaster.matrix/tests/testthat/test-stage-matrix.R
@@ -128,33 +128,3 @@
expect_identical(DelayedArray::type(mat2), "logical")
expect_identical(as.matrix(mat), as.matrix(mat2))
})
-
-test_that("stageObject works with DelayedMatrices (naive)", {
- dir <- tempfile()
- odir <- file.path(dir, experiment)
- dir.create(odir, recursive=TRUE)
-
- # Works in the pristine case, where it just extracts the seed.
- library(DelayedArray)
- mat <- as(matrix(rpois(10000, 1), ncol=10), "dgCMatrix")
- x <- DelayedArray(mat)
-
- info <- stageObject(x, dir, file.path(experiment, assay))
- expect_match(info$`$schema`, "sparse_matrix")
- expect_error(alabaster.base::.writeMetadata(info, dir), NA)
-
- mat2 <- loadArray(info, project=dir)
- expect_equal(unname(as.matrix(mat2)), unname(as.matrix(x)))
- expect_null(rownames(mat2))
- expect_null(colnames(mat2))
-
- # Works with assigned dimnames.
- y <- x
- dimnames(y) <- list(seq_len(nrow(y)), LETTERS[1:10])
-
- info <- stageObject(y, dir, file.path(experiment, "other"))
- expect_error(alabaster.base::.writeMetadata(info, dir), NA)
-
- mat2 <- loadArray(info, project=dir)
- expect_equal(as.matrix(mat2), as.matrix(y))
-})
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