R Under development (unstable) (2024-09-02 r87090 ucrt) -- "Unsuffered Consequences"
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> library("matrixStats")
> 
> rowSums2_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
+   ## FIXME: sum() may overflow for integers, whereas
+   ## base::rowSums() doesn't.  What should rowSums2() do?
+   ## apply(x, MARGIN = 1L, FUN = sum, na.rm = na.rm)
+   res <- rowSums(x, na.rm = na.rm)
+   if (is.na(useNames) || !useNames) names(res) <- NULL
+   res
+ }
> 
> colSums2_R <- function(x, na.rm = FALSE, ..., useNames = NA) {
+   ## FIXME: sum() may overflow for integers, whereas
+   ## base::colSums() doesn't.  What should colSums2() do?
+   ## apply(x, MARGIN = 2L, FUN = sum, na.rm = na.rm)
+   res <- colSums(x, na.rm = na.rm)
+   if (is.na(useNames) || !useNames) names(res) <- NULL
+   res
+ }
> 
> for (mode in c("integer", "logical", "double")) {
+   x <- matrix(-4:4, nrow = 3, ncol = 3)
+   storage.mode(x) <- mode
+   if (mode == "double") x <- x + 0.1
+   
+   # To check names attribute
+   dimnames <- list(letters[1:3], LETTERS[1:3])
+   
+   # Test with and without dimnames on x
+   for (setDimnames in c(TRUE, FALSE)) {
+     if (setDimnames) dimnames(x) <- dimnames
+     else dimnames(x) <- NULL
+     # Check names attribute
+     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+       y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
+       y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
+       stopifnot(all.equal(y1, y0))
+       
+       y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
+       y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
+       stopifnot(all.equal(y1, y0))
+     }
+   }
+ }
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: Single-element matrix
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: Single-element matrix:\n")
Special case: Single-element matrix:
> for (mode in c("integer", "logical", "double")) {
+   x <- matrix(1, nrow = 1, ncol = 1)
+   storage.mode(x) <- mode
+   
+   # To check names attribute
+   dimnames <- list("a", "A")
+   
+   # Test with and without dimnames on x
+   for (setDimnames in c(TRUE, FALSE)) {
+     if (setDimnames) dimnames(x) <- dimnames
+     else dimnames(x) <- NULL
+     # Check names attribute
+     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+       y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
+       y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
+       stopifnot(all.equal(y1, y0))
+       
+       y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
+       y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
+       stopifnot(all.equal(y1, y0))
+     }
+   }
+ }
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: Empty matrix
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: Empty matrix:\n")
Special case: Empty matrix:
> for (mode in c("integer", "logical", "double")) {
+   x <- matrix(integer(0), nrow = 0, ncol = 0)
+   storage.mode(x) <- mode
+ 
+   y0 <- rowSums2_R(x, na.rm = FALSE)
+   y1 <- rowSums2(x, na.rm = FALSE)
+   stopifnot(all.equal(y1, y0))
+ 
+   y0 <- colSums2_R(x, na.rm = FALSE)
+   y1 <- colSums2(x, na.rm = FALSE)
+   stopifnot(all.equal(y1, y0))
+ }
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: All NAs
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: All NAs:\n")
Special case: All NAs:
> for (mode in c("integer", "logical", "double")) {
+   x <- matrix(NA_integer_, nrow = 3, ncol = 3)
+   storage.mode(x) <- mode
+   
+   # To check names attribute
+   dimnames <- list(letters[1:3], LETTERS[1:3])
+   
+   # Test with and without dimnames on x
+   for (setDimnames in c(TRUE, FALSE)) {
+     if (setDimnames) dimnames(x) <- dimnames
+     else dimnames(x) <- NULL
+     # Check names attribute
+     for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+       y0 <- rowSums2_R(x, na.rm = TRUE, useNames = useNames)
+       y1 <- rowSums2(x, na.rm = TRUE, useNames = useNames)
+       stopifnot(all.equal(y1, y0))
+       
+       y0 <- colSums2_R(x, na.rm = TRUE, useNames = useNames)
+       y1 <- colSums2(x, na.rm = TRUE, useNames = useNames)
+       stopifnot(all.equal(y1, y0))
+     }
+   }
+ }
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: All NaNs
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: All NaNs:\n")
Special case: All NaNs:
> x <- matrix(NA_real_, nrow = 3, ncol = 3)
> 
> # Test with and without dimnames on x
> for (setDimnames in c(TRUE, FALSE)) {
+   if (setDimnames) dimnames(x) <- dimnames
+   else dimnames(x) <- NULL
+   # Check names attribute
+   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+     y0 <- rowSums2_R(x, na.rm = TRUE, useNames = useNames)
+     y1 <- rowSums2(x, na.rm = TRUE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+     
+     y0 <- colSums2_R(x, na.rm = TRUE, useNames = useNames)
+     y1 <- colSums2(x, na.rm = TRUE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+   }
+ }
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: All Infs
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: All Infs:\n")
Special case: All Infs:
> x <- matrix(Inf, nrow = 3, ncol = 3)
> 
> # Test with and without dimnames on x
> for (setDimnames in c(TRUE, FALSE)) {
+   if (setDimnames) dimnames(x) <- dimnames
+   else dimnames(x) <- NULL
+   # Check names attribute
+   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
+     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+     
+     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
+     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+   }
+ }
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: All -Infs
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: All -Infs:\n")
Special case: All -Infs:
> x <- matrix(-Inf, nrow = 3, ncol = 3)
> 
> # Test with and without dimnames on x
> for (setDimnames in c(TRUE, FALSE)) {
+   if (setDimnames) dimnames(x) <- dimnames
+   else dimnames(x) <- NULL
+   # Check names attribute
+   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
+     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+     
+     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
+     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+   }
+ }
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: Infs and -Infs
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: Infs and -Infs:\n")
Special case: Infs and -Infs:
> x <- matrix(c(-Inf, +Inf), nrow = 4, ncol = 4)
> 
> # To check names attribute
> dimnames <- list(letters[1:4], LETTERS[1:4])
> 
> # Test with and without dimnames on x
> for (setDimnames in c(TRUE, FALSE)) {
+   if (setDimnames) dimnames(x) <- dimnames
+   else dimnames(x) <- NULL
+   # Check names attribute
+   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
+     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+     
+     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
+     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+   }
+ }
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: NaNs and NAs
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: Infs and -Infs:\n")
Special case: Infs and -Infs:
> x <- matrix(c(NaN, NA_real_), nrow = 4, ncol = 4)
> 
> y0 <- rowSums(x, na.rm = FALSE)
> str(y0)
 num [1:4] NaN NA NaN NA
> stopifnot(all(is.na(y0)), length(unique(y0)) >= 1L)
> y1 <- rowSums2(x, na.rm = FALSE)
> str(y0)
 num [1:4] NaN NA NaN NA
> stopifnot(all(is.na(y1)), length(unique(y1)) >= 1L)
> stopifnot(all.equal(y1, y0))
> 
> y0 <- colSums(x, na.rm = FALSE)
> stopifnot(all(is.na(y0)), length(unique(y0)) == 1L)
> y1 <- colSums2(x, na.rm = FALSE)
> stopifnot(all(is.na(y1)), length(unique(y1)) == 1L)
> ## NOTE, due to compiler optimization, it is not guaranteed that NA is
> ## returned here (as one would expect). NaN might very well be returned,
> ## when both NA and NaN are involved.  This is an accepted feature in R,
> ## which is documented in help("is.nan").  See also
> ## https://stat.ethz.ch/pipermail/r-devel/2017-April/074009.html.
> ## Thus, we cannot guarantee that y1 is identical to y0.
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Special case: Integer overflow with ties
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> cat("Special case: Integer overflow with ties:\n")
Special case: Integer overflow with ties:
> x <- matrix(.Machine$integer.max, nrow = 4, ncol = 4)
> 
> # Test with and without dimnames on x
> for (setDimnames in c(TRUE, FALSE)) {
+   if (setDimnames) dimnames(x) <- dimnames
+   else dimnames(x) <- NULL
+   # Check names attribute
+   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+     y0 <- rowSums2_R(x, na.rm = FALSE, useNames = useNames)
+     y1 <- rowSums2(x, na.rm = FALSE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+     
+     y0 <- colSums2_R(x, na.rm = FALSE, useNames = useNames)
+     y1 <- colSums2(x, na.rm = FALSE, useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+   }
+ }
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Consistency checks
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> set.seed(1)
> 
> cat("Consistency checks:\n")
Consistency checks:
> n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 4L else 20L
> for (kk in seq_len(n_sims)) {
+   cat("Random test #", kk, "\n", sep = "")
+ 
+   # Simulate data in a matrix of any shape
+   dim <- sample(50:200, size = 2)
+   n <- prod(dim)
+   x <- rnorm(n, sd = 100)
+   dim(x) <- dim
+ 
+   # Add NAs?
+   if ((kk %% 4) %in% c(3, 0)) {
+     cat("Adding NAs\n")
+     nna <- sample(n, size = 1)
+     na_values <- c(NA_real_, NaN)
+     t <- sample(na_values, size = nna, replace = TRUE)
+     x[sample(length(x), size = nna)] <- t
+   }
+ 
+   # Mode?
+   modes <- "double"
+   if ((kk %% 4) %in% c(2, 0)) {
+     modes <- c("integer", "logical")
+   }
+ 
+   for (mode in modes) {
+     if (mode != "double") {
+       cat(sprintf("Coercing from %s to %s\n", storage.mode(x), mode))
+       storage.mode(x) <- mode
+     }
+ 
+     na.rm <- sample(c(TRUE, FALSE), size = 1)
+   
+     # rowSums2():
+     y0 <- rowSums2_R(x, na.rm = na.rm)
+     y1 <- rowSums2(x, na.rm = na.rm)
+     stopifnot(all.equal(y1, y0))
+     y2 <- colSums2(t(x), na.rm = na.rm)
+     stopifnot(all.equal(y2, y0))
+   
+     # colSums2():
+     y0 <- colSums2_R(x, na.rm = na.rm)
+     y1 <- colSums2(x, na.rm = na.rm)
+     stopifnot(all.equal(y1, y0))
+     y2 <- rowSums2(t(x), na.rm = na.rm)
+     stopifnot(all.equal(y2, y0))
+   }
+ } # for (kk ...)
Random test #1
Random test #2
Coercing from double to integer
Coercing from integer to logical
Random test #3
Adding NAs
Random test #4
Adding NAs
Coercing from double to integer
Coercing from integer to logical
Random test #5
Random test #6
Coercing from double to integer
Coercing from integer to logical
Random test #7
Adding NAs
Random test #8
Adding NAs
Coercing from double to integer
Coercing from integer to logical
Random test #9
Random test #10
Coercing from double to integer
Coercing from integer to logical
Random test #11
Adding NAs
Random test #12
Adding NAs
Coercing from double to integer
Coercing from integer to logical
Random test #13
Random test #14
Coercing from double to integer
Coercing from integer to logical
Random test #15
Adding NAs
Random test #16
Adding NAs
Coercing from double to integer
Coercing from integer to logical
Random test #17
Random test #18
Coercing from double to integer
Coercing from integer to logical
Random test #19
Adding NAs
Random test #20
Adding NAs
Coercing from double to integer
Coercing from integer to logical
> 
> proc.time()
   user  system elapsed 
   0.43    0.10    0.48