context("importCdf") ## create NetCDF test file # #library("RNetCDF") #nc <- create.nc("tiny.cdf") # #dim.def.nc(nc, "scan_number", 2) #dim.def.nc(nc, "point_number", 10, unlim=TRUE) # #var.def.nc(nc, "scan_index", "NC_INT", "scan_number") #var.def.nc(nc, "point_count", "NC_INT", "scan_number") #var.def.nc(nc, "scan_acquisition_time", "NC_DOUBLE", "scan_number") # #var.def.nc(nc, "mass_values", "NC_DOUBLE", "point_number") #var.def.nc(nc, "intensity_values", "NC_INT", "point_number") # #var.put.nc(nc, "scan_index", c(0,5)) #var.put.nc(nc, "point_count", c(5, 5)) #var.put.nc(nc, "scan_acquisition_time", c(1, 2)) # #var.put.nc(nc, "mass_values", 1:5, start=1, count=5) #var.put.nc(nc, "mass_values", 6:10, start=6, count=5) #var.put.nc(nc, "intensity_values", 11:15, start=1, count=5) #var.put.nc(nc, "intensity_values", 16:20, start=6, count=5) # #close.nc(nc) # test_that("importCdf", { path <- normalizePath(system.file(file.path("exampledata", "tiny.cdf"), package="MALDIquantForeign")) if (suppressWarnings(require("RNetCDF", quietly=TRUE))) { ## suppress warnings to avoid creation of Rplots.pdf expect_error(suppressWarnings(MALDIquantForeign:::.importCdf("tmp.tmp"))) r <- list(createMassSpectrum(mass=1:5, intensity=11:15, metaData=list(file=path, number=1, retentionTime=1, scanIndex=0)), createMassSpectrum(mass=6:10, intensity=16:20, metaData=list(file=path, number=2, retentionTime=2, scanIndex=5))) s <- MALDIquantForeign:::.importCdf(path, verbose=FALSE) expect_equal(s, import(path, verbose=FALSE)) expect_equal(s, importCdf(path, verbose=FALSE)) expect_equal(s, import(path, type="cdf", verbose=FALSE)) expect_equal(mass(s[[1]]), 1:5) expect_equal(intensity(s[[1]]), 11:15) expect_equal(basename(metaData(s[[1]])$file), "tiny.cdf") expect_equal(s, r) } else { expect_error(suppressWarnings(MALDIquantForeign:::.importCdf(path)), "install.packages") } })
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