################################################################################ context("FBM_CONVERT") opt.save <- options(bigstatsr.downcast.warning = TRUE) set.seed(SEED) ################################################################################ to_gen <- function(x) { if (gen == "scalar") { `if`(typeof(x) == "double", x[1]^2, x[1]) } else if (gen == "vector") { x } else { dim(x) <- c(10, 10) x } } gen <- "scalar" expect_identical(to_gen(1:10), 1L) gen <- "vector" expect_identical(to_gen(1:10), 1:10) gen <- "matrix" expect_identical(to_gen(1:100), matrix(1:100, 10)) ################################################################################ expect_FBM <- function(expr) { res <- eval.parent(substitute(expr)) expect_s4_class(res, class = "FBM") } expect_warning(FBM(10, 10, "raw", runif(100))) if (exists("XX")) rm("XX") expect_false(exists("XX")) expect_FBM(without_downcast_warning(XX <- FBM(10, 10, "raw", runif(100)))) expect_true(exists("XX")) ################################################################################ test_that("Downcast warnings work", { skip_if_not(not_cran) get_text <- function(rtype, ctype) { sprintf("while converting from R type '%s' to C type '%s'.", rtype, ctype) } for (gen in c("scalar", "vector", "matrix")) { # From double x1 <- to_gen(runif(100)) # To raw expect_warning(X <- FBM(10, 10, x1, type = "raw"), get_text("double", "unsigned char (raw)"), fixed = TRUE) expect_warning(X[1:5] <- x1[1:5], get_text("double", "unsigned char (raw)"), fixed = TRUE) expect_warning(X[2] <- NA_real_, get_text("double", "unsigned char (raw)"), fixed = TRUE) expect_FBM(without_downcast_warning( FBM(10, 10, x1, type = "raw") )) # To ushort expect_warning(X <- FBM(10, 10, x1, type = "unsigned short"), get_text("double", "unsigned short"), fixed = TRUE) expect_warning(X[1:5] <- x1[1:5], get_text("double", "unsigned short"), fixed = TRUE) expect_warning(X[2] <- NA_real_, get_text("double", "unsigned short"), fixed = TRUE) expect_FBM(without_downcast_warning( FBM(10, 10, x1, type = "unsigned short") )) # To int expect_warning(X <- FBM(10, 10, x1, type = "integer"), get_text("double", "integer"), fixed = TRUE) expect_warning(X[1:5] <- x1[1:5], get_text("double", "integer"), fixed = TRUE) X[2] <- NA_real_ expect_identical(X[2], NA_integer_) expect_warning(X[2] <- Inf, get_text("double", "integer"), fixed = TRUE) expect_warning(X[2] <- NaN, get_text("double", "integer"), fixed = TRUE) expect_FBM(without_downcast_warning( FBM(10, 10, x1, type = "integer") )) # To float expect_warning(X <- FBM(10, 10, x1, type = "float")) X[2] <- NA_real_ expect_identical(X[2], NA_real_) # To double expect_FBM(X <- FBM(10, 10, x1, type = "double")) expect_identical(X[1:5] <- x1[1:5], x1[1:5]) X[2] <- NA_real_ expect_identical(X[2], NA_real_) # From integer x2 <- to_gen(1:100 + 1e6L) # To raw expect_warning(X <- FBM(10, 10, x2, type = "raw"), get_text("integer", "unsigned char (raw)"), fixed = TRUE) expect_warning(X[1:5] <- x2[1:5], get_text("integer", "unsigned char (raw)"), fixed = TRUE) expect_warning(X[2] <- NA_integer_, get_text("integer", "unsigned char (raw)"), fixed = TRUE) expect_FBM(without_downcast_warning( FBM(10, 10, x2, type = "raw") )) # To ushort expect_warning(X <- FBM(10, 10, x2, type = "unsigned short"), get_text("integer", "unsigned short"), fixed = TRUE) expect_warning(X[1:5] <- x2[1:5], get_text("integer", "unsigned short"), fixed = TRUE) expect_warning(X[2] <- NA_integer_, get_text("integer", "unsigned short"), fixed = TRUE) expect_FBM(without_downcast_warning( FBM(10, 10, x2, type = "unsigned short") )) # To int expect_FBM(X <- FBM(10, 10, x2, type = "integer")) expect_identical(X[1:5] <- x2[1:5], x2[1:5]) X[2] <- NA_integer_ expect_identical(X[2], NA_integer_) # To float expect_FBM(X <- FBM(10, 10, x2, type = "float")) expect_identical(X[1:5] <- x2[1:5], x2[1:5]) X[2] <- NA_integer_ expect_identical(X[2], NA_real_) # To double expect_FBM(X <- FBM(10, 10, x2, type = "double")) expect_identical(X[1:5] <- x2[1:5], x2[1:5]) X[2] <- NA_integer_ expect_identical(X[2], NA_real_) # From logical x3 <- to_gen(sample(c(TRUE, FALSE), 100, TRUE)) # To raw expect_FBM(X <- FBM(10, 10, x3, type = "raw")) expect_identical(X[1:5] <- na.omit(x3[1:5]), na.omit(x3[1:5])) expect_warning(X[2] <- NA, get_text("logical", "unsigned char (raw)"), fixed = TRUE) # To ushort expect_FBM(X <- FBM(10, 10, x3, type = "unsigned short")) expect_identical(X[1:5] <- na.omit(x3[1:5]), na.omit(x3[1:5])) expect_warning(X[2] <- NA, get_text("logical", "unsigned short"), fixed = TRUE) # To int expect_FBM(X <- FBM(10, 10, x3, type = "integer")) expect_identical(X[1:5] <- x3[1:5], x3[1:5]) X[2] <- NA expect_identical(X[2], NA_integer_) # To float expect_FBM(X <- FBM(10, 10, x3, type = "float")) expect_identical(X[1:5] <- x3[1:5], x3[1:5]) X[2] <- NA expect_identical(X[2], NA_real_) # To double expect_FBM(X <- FBM(10, 10, x3, type = "double")) expect_identical(X[1:5] <- x3[1:5], x3[1:5]) X[2] <- NA expect_identical(X[2], NA_real_) # From raw x4 <- to_gen(sample(as.raw(0:255), 100, TRUE)) expect_FBM(X <- FBM(10, 10, x4, type = "raw")) expect_identical(X[1:5] <- x4[1:5], x4[1:5]) expect_FBM(X <- FBM(10, 10, x4, type = "unsigned short")) expect_identical(X[1:5] <- x4[1:5], x4[1:5]) expect_FBM(X <- FBM(10, 10, x4, type = "integer")) expect_identical(X[1:5] <- x4[1:5], x4[1:5]) expect_FBM(X <- FBM(10, 10, x4, type = "float")) expect_identical(X[1:5] <- x4[1:5], x4[1:5]) expect_FBM(X <- FBM(10, 10, x4, type = "double")) expect_identical(X[1:5] <- x4[1:5], x4[1:5]) } }) ################################################################################ test_that("Missing values transfer from int to double", { for (t in c("float", "double")) { for (na in list(NA, NA_integer_, NA_real_)) { a <- matrix(na, 7, 11) A <- as_FBM(a, type = "double") A[] <- a expect_true(all(is.na(A[]))) A[] <- as.vector(a) expect_true(all(is.na(A[]))) A[] <- a[1] expect_true(all(is.na(A[]))) A[] <- matrix(a[1], 1, 1) expect_true(all(is.na(A[]))) A[1:5] <- a[1:5] expect_true(all(is.na(A[1:5]))) A[1:5] <- matrix(a[1:5], 5, 1) expect_true(all(is.na(A[1:5]))) A[1:5] <- a[5] expect_true(all(is.na(A[1:5]))) A[1:5] <- matrix(a[5], 1, 1) expect_true(all(is.na(A[1:5]))) A[2] <- a[2] expect_identical(A[2], NA_real_) } } }) ################################################################################ test_that("Special values are handled for floats", { expect_identical(expect_warning(FBM(1, 1, "float", 2^-126), "NA")[], NA_real_) expect_warning(FBM(1, 1, "float", 1.175494e-38)[]) expect_warning(FBM(1, 1, "float", 1.1754943e-38)[]) expect_warning(FBM(1, 1, "float", 0.51)) expect_identical(FBM(1, 1, "float", 0.5)[], 0.5) expect_identical(FBM(1, 1, "float", 2^-149)[], 2^-149) expect_identical(FBM(1, 1, "float", NA)[], NA_real_) expect_identical(FBM(1, 1, "float", NA_integer_)[], NA_real_) expect_identical(FBM(1, 1, "float", NA_real_)[], NA_real_) expect_identical(FBM(1, 1, "float", Inf)[], Inf) expect_identical(FBM(1, 1, "float", -Inf)[], -Inf) expect_identical(FBM(1, 1, "float", NaN)[], NaN) }) ################################################################################ test_that("No copy is made", { options(bigstatsr.downcast.warning = FALSE) N <- M <- 2000 size <- N * M * 8 / 1024^2 x4 <- matrix(round(rnorm(N * M, 100, 10)), N) x3 <- x2 <- x1 <- x4 storage.mode(x1) <- "raw" storage.mode(x2) <- "logical" storage.mode(x3) <- "integer" X5 <- big_copy(x4, type = "double") X4 <- big_copy(x4, type = "float") X3 <- big_copy(x4, type = "integer") X2 <- big_copy(x4, type = "unsigned short") X1 <- big_copy(x4, type = "unsigned char") tmp <- gc(reset = TRUE) x <- x3 + 0 expect_gt((gc() - tmp)[2, 6], size / 10) # print(size) for (X in list(X1, X2, X3, X4, X5)) { # print(typeof(X)) for (x in list(x1, x2, x3, x4)) { tmp <- gc(reset = TRUE) X[] <- x diff <- gc() - tmp mb <- tail(diff["Vcells", ], 1) expect_true(names(mb) == "(Mb)") expect_lt(mb, size / 10) } } }) ################################################################################ options(opt.save) ################################################################################