STYLE: More lintr style

.make/Makefile

@@ -56,6 +56,7 @@ R_NO_INIT := --no-init-file
 R_VERSION_STATUS := $(shell $(R_SCRIPT) -e "status <- tolower(R.version[['status']]); if (regexpr('unstable', status) != -1L) status <- 'devel'; cat(status)")
 R_VERSION_X_Y := $(shell $(R_SCRIPT) -e "cat(gsub('[.][0-9]+$$', '', getRversion()))")
 R_VERSION := $(shell $(R_SCRIPT) -e "cat(as.character(getRversion()))")
+R_VERSION_3_3_OR_NEWER := $(shell $(R_SCRIPT) -e "cat(getRversion() >= '3.3.0')")
 R_VERSION_FULL := $(R_VERSION)$(R_VERSION_STATUS)
 R_LIBS_USER_X := $(shell $(R_SCRIPT) -e "cat(.libPaths()[1])")
 R_INCLUDE := $(shell $(R_SCRIPT) -e "cat(R.home('include'))")
@@ -79,6 +80,16 @@ GIT_COMMIT := $(shell $(GIT) log -1 --format="%h")
 R_LIBS_BRANCH := $(CURDIR)/.R/$(GIT_BRANCH)
 
 
+# Asserts proper Windows toolchain in R (>= 3.3.0)
+ifeq ($(OS), Windows_NT)
+ifeq ($(R_VERSION_3_3_OR_NEWER), TRUE)
+ifndef BINPREF
+$(error R (>= 3.3.0) on Windows: BINPREF not set)
+endif
+endif
+endif
+
+
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # Main
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
@@ -123,6 +134,7 @@ debug:
 	@echo R_RD4PDF=\'$(R_RD4PDF)\'
 	@echo
 	@echo R_CRAN_OUTDIR=\'$(R_CRAN_OUTDIR)\'
+	@echo R_VERSION_3_3_OR_NEWER=\'$(R_VERSION_3_3_OR_NEWER)\'
 	@echo
 
 
@@ -326,6 +338,12 @@ $(R_OUTDIR)/vigns: install
 vignettes: $(R_OUTDIR)/vigns
 
 
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# Static code validation etc
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+lint:
+	$(R_SCRIPT) -e "library(lintr); lint_package(linters = with_defaults(commented_code_linter = NULL, closed_curly_linter = closed_curly_linter(allow_single_line = TRUE), open_curly_linter = open_curly_linter(allow_single_line = TRUE)))"
+
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # Run package tests
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

R/rowIQRs.R

@@ -61,7 +61,7 @@ iqr <- function(x, idxs = NULL, na.rm = FALSE, ...) {
   # Apply subset
   if (!is.null(idxs)) x <- x[idxs]
 
-  if(na.rm) {
+  if (na.rm) {
     x <- x[!is.na(x)]
   } else if (anyMissing(x)) {
     return(NA_real_)

R/varDiff.R

@@ -188,7 +188,7 @@ iqrDiff <- function(x, idxs = NULL, na.rm = FALSE, diff = 1L, trim = 0, ...) {
   # Apply subset
   if (!is.null(idxs)) x <- x[idxs]
 
-  if(na.rm) {
+  if (na.rm) {
     x <- x[!is.na(x)]
   } else if (anyMissing(x)) {
     return(NA_real_)

tests/allocArray.R

@@ -6,7 +6,9 @@ allocArray_R <- function(nrow, ncol, value = NA) {
 
 values <- list(
   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
-  -1, 0, +1, NA_real_, NaN, -Inf, +Inf, .Machine$double.xmin, .Machine$double.xmax, .Machine$double.eps, .Machine$double.neg.eps,
+  -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
+  .Machine$double.xmin, .Machine$double.xmax,
+  .Machine$double.eps, .Machine$double.neg.eps,
   FALSE, TRUE, NA
 )
 

tests/allocMatrix.R

@@ -6,7 +6,9 @@ allocMatrix_R <- function(nrow, ncol, value = NA) {
 
 values <- list(
   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
-  -1, 0, +1, NA_real_, NaN, -Inf, +Inf, .Machine$double.xmin, .Machine$double.xmax, .Machine$double.eps, .Machine$double.neg.eps,
+  -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
+  .Machine$double.xmin, .Machine$double.xmax,
+  .Machine$double.eps, .Machine$double.neg.eps,
   FALSE, TRUE, NA
 )
 

tests/allocVector.R

@@ -8,7 +8,9 @@ allocVector_R <- function(length, value = NA) {
 
 values <- list(
   -1L, 0L, +1L, NA_integer_, .Machine$integer.max,
-  -1, 0, +1, NA_real_, NaN, -Inf, +Inf, .Machine$double.xmin, .Machine$double.xmax, .Machine$double.eps, .Machine$double.neg.eps,
+  -1, 0, +1, NA_real_, NaN, -Inf, +Inf,
+  .Machine$double.xmin, .Machine$double.xmax,
+  .Machine$double.eps, .Machine$double.neg.eps,
   FALSE, TRUE, NA
 )
 

tests/anyMissing_subset.R

@@ -9,7 +9,8 @@ x[2] <- NA
 for (mode in c("integer", "numeric")) {
   storage.mode(x) <- mode
   for (idxs in indexCases) {
-    validateIndicesTestVector(x, idxs, ftest = anyMissing, fsure = function(x, ...) {
+    validateIndicesTestVector(x, idxs,
+                              ftest = anyMissing, fsure = function(x, ...) {
         anyValue(x, value = NA)
     })
   }

tests/binCounts.R

@@ -5,7 +5,8 @@ library("stats")
 # Local functions
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 binCounts_hist <- function(x, bx, right = FALSE, ...) {
-  n0 <- graphics::hist(x, breaks = bx, right = right, include.lowest = TRUE, plot = FALSE)$counts
+  n0 <- graphics::hist(x, breaks = bx, right = right,
+                       include.lowest = TRUE, plot = FALSE)$counts
 }
 
 

tests/binMeans,binCounts_subset.R

@@ -42,7 +42,13 @@ storage.mode(x) <- "integer"
 bx <- c(-6, 0, 3, 4, 10)
 for (idxs in indexCases) {
   for (na.rm in c(TRUE, FALSE)) {
-    validateIndicesTestVector_w(y, x, idxs, ftest = binMeans, fsure = binMeans0, bx = bx, na.rm = na.rm, count = TRUE, right = FALSE)
-    validateIndicesTestVector_w(y, x, idxs, ftest = binMeans, fsure = binMeans0, bx = bx, na.rm = na.rm, count = TRUE, right = TRUE)
+    validateIndicesTestVector_w(y, x, idxs,
+                                ftest = binMeans, fsure = binMeans0,
+                                bx = bx, na.rm = na.rm,
+                                count = TRUE, right = FALSE)
+    validateIndicesTestVector_w(y, x, idxs,
+                                ftest = binMeans, fsure = binMeans0,
+                                bx = bx, na.rm = na.rm,
+                                count = TRUE, right = TRUE)
   }
 }

tests/count_subset.R

@@ -17,7 +17,13 @@ source("utils/validateIndicesFramework.R")
 x <- runif(6, min = -3, max = 3)
 storage.mode(x) <- "integer"
 for (idxs in indexCases) {
-  validateIndicesTestVector(x, idxs, ftest = count, fsure = count_R, value = 0, na.rm = TRUE)
-  validateIndicesTestVector(x, idxs, ftest = count, fsure = count_R, value = 0, na.rm = FALSE)
-  validateIndicesTestVector(x, idxs, ftest = count, fsure = count_R, value = NA_integer_)
+  validateIndicesTestVector(x, idxs,
+                            ftest = count, fsure = count_R,
+                            value = 0, na.rm = TRUE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = count, fsure = count_R,
+                            value = 0, na.rm = FALSE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = count, fsure = count_R,
+                            value = NA_integer_)
 }

tests/diff2.R

@@ -14,7 +14,8 @@ for (mode in c("integer", "double")) {
 
     for (l in 1:3) {
       for (d in 1:4) {
-        cat(sprintf("%s: NAs = %s, lag = %d, differences = %d\n", mode, hasNA, l, d))
+        cat(sprintf("%s: NAs = %s, lag = %d, differences = %d\n",
+                    mode, hasNA, l, d))
         y0 <- diff(x, lag = l, differences = d)
         str(y0)
         y1 <- diff2(x, lag = l, differences = d)

tests/diff2_subset.R

@@ -8,7 +8,9 @@ x <- runif(6, min = -6, max = 6)
 for (l in 1:2) {
   for (d in 1:2) {
     for (idxs in indexCases) {
-      validateIndicesTestVector(x, idxs, ftest = diff2, fsure = diff, lag = l, differences = d)
+      validateIndicesTestVector(x, idxs,
+                                ftest = diff2, fsure = diff,
+                                lag = l, differences = d)
     }
   }
 }

tests/logSumExp_subset.R

@@ -11,6 +11,10 @@ logSumExp_R <- function(lx, na.rm = FALSE) {
 source("utils/validateIndicesFramework.R")
 x <- runif(6, min = -6, max = 6)
 for (idxs in indexCases) {
-  validateIndicesTestVector(x, idxs, ftest = logSumExp, fsure = logSumExp_R, na.rm = FALSE)
-  validateIndicesTestVector(x, idxs, ftest = logSumExp, fsure = logSumExp_R, na.rm = TRUE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = logSumExp, fsure = logSumExp_R,
+                            na.rm = FALSE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = logSumExp, fsure = logSumExp_R,
+                            na.rm = TRUE)
 }

tests/meanOver.R

@@ -27,7 +27,8 @@ for (kk in 1:20) {
     cat("Adding NAs\n")
     nna <- sample(n, size = 1L)
     naValues <- c(NA_real_, NaN)
-    x[sample(length(x), size = nna)] <- sample(naValues, size = nna, replace = TRUE)
+    t <- sample(naValues, size = nna, replace = TRUE)
+    x[sample(length(x), size = nna)] <- t
   }
 
   # Integer or double?

tests/meanOver_subset.R

@@ -7,6 +7,10 @@ source("utils/validateIndicesFramework.R")
 x <- runif(6, min = -6, max = 6)
 storage.mode(x) <- "integer"
 for (idxs in indexCases) {
-  validateIndicesTestVector(x, idxs, ftest = meanOver, fsure = mean, na.rm = FALSE)
-  validateIndicesTestVector(x, idxs, ftest = meanOver, fsure = mean, na.rm = TRUE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = meanOver, fsure = mean,
+                            na.rm = FALSE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = meanOver, fsure = mean,
+                            na.rm = TRUE)
 }

tests/product_subset.R

@@ -7,6 +7,10 @@ source("utils/validateIndicesFramework.R")
 x <- runif(6, min = -6, max = 6)
 storage.mode(x) <- "integer"
 for (idxs in indexCases) {
-  validateIndicesTestVector(x, idxs, ftest = product, fsure = prod, na.rm = TRUE)
-  validateIndicesTestVector(x, idxs, ftest = product, fsure = prod, na.rm = FALSE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = product, fsure = prod,
+                            na.rm = TRUE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = product, fsure = prod,
+                            na.rm = FALSE)
 }

tests/psortKM.R

@@ -1,5 +1,5 @@
 library("matrixStats")
-library("utils")
+library("utils")  ## utils::str
 
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 # Local functions

tests/rowCollapse.R

@@ -23,7 +23,8 @@ stopifnot(identical(y2, y))
 idxs <- 1:3
 y <- rowCollapse(x, idxs)
 print(y)
-yT <- c(x[1, 1], x[2, 2], x[3, 3], x[4, 1], x[5, 2], x[6, 3], x[7, 1], x[8, 2], x[9, 3])
+yT <- c(x[1, 1], x[2, 2], x[3, 3], x[4, 1], x[5, 2],
+        x[6, 3], x[7, 1], x[8, 2], x[9, 3])
 stopifnot(identical(y, yT))
 y2 <- colCollapse(t(x), idxs)
 stopifnot(identical(y2, y))

tests/rowCounts.R

@@ -2,9 +2,13 @@ library("matrixStats")
 
 rowCounts_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
   if (is.na(value)) {
-    counts <- apply(x, MARGIN = 1L, FUN = function(x) sum(is.na(x)))
+    counts <- apply(x, MARGIN = 1L, FUN = function(x)
+      sum(is.na(x))
+    )
   } else {
-    counts <- apply(x, MARGIN = 1L, FUN = function(x) sum(x == value, na.rm = na.rm))
+    counts <- apply(x, MARGIN = 1L, FUN = function(x)
+      sum(x == value, na.rm = na.rm)
+    )
   }
   as.integer(counts)
 } # rowCounts_R()

tests/rowCounts_subset.R

@@ -2,9 +2,13 @@ library("matrixStats")
 
 rowCounts_R <- function(x, value = TRUE, na.rm = FALSE, ...) {
   if (is.na(value)) {
-    counts <- apply(x, MARGIN = 1L, FUN = function(x) sum(is.na(x)))
+    counts <- apply(x, MARGIN = 1L, FUN = function(x)
+      sum(is.na(x))
+    )
   } else {
-    counts <- apply(x, MARGIN = 1L, FUN = function(x) sum(x == value, na.rm = na.rm))
+    counts <- apply(x, MARGIN = 1L, FUN = function(x)
+      sum(x == value, na.rm = na.rm)
+    )
   }
   as.integer(counts)
 } # rowCounts_R()

tests/rowDiffs.R

@@ -34,7 +34,8 @@ for (mode in c("integer", "double")) {
 
     for (lag in 1:4) {
       for (differences in 1:3) {
-        cat(sprintf("mode: %s, lag = %d, differences = %d\n", mode, lag, differences))
+        cat(sprintf("mode: %s, lag = %d, differences = %d\n",
+                    mode, lag, differences))
         # Row/column ranges
         r0 <- rowDiffs_R(x, lag = lag, differences = differences)
         r1 <- rowDiffs(x, lag = lag, differences = differences)

tests/rowMedians.R

@@ -195,7 +195,8 @@ for (kk in seq_len(K)) {
     cat("Adding NAs\n")
     nna <- sample(n, size = 1)
     naValues <- c(NA_real_, NaN)
-    x[sample(length(x), size = nna)] <- sample(naValues, size = nna, replace = TRUE)
+    t <- sample(naValues, size = nna, replace = TRUE)
+    x[sample(length(x), size = nna)] <- t
   }
 
   # Integer or double?

tests/rowProds_subset.R

@@ -1,8 +1,7 @@
 library("matrixStats")
 
 rowProds_R <- function(x, FUN = prod, na.rm = FALSE, ...) {
-  y <- apply(x, MARGIN = 1L, FUN = FUN, na.rm = na.rm)
-  y
+  apply(x, MARGIN = 1L, FUN = FUN, na.rm = na.rm)
 }
 
 

tests/rowQuantiles.R

@@ -87,7 +87,8 @@ for (kk in seq_len(K)) {
     cat("Adding NAs\n")
     nna <- sample(n, size = 1)
     naValues <- c(NA_real_, NaN)
-    x[sample(length(x), size = nna)] <- sample(naValues, size = nna, replace = TRUE)
+    t <- sample(naValues, size = nna, replace = TRUE)
+    x[sample(length(x), size = nna)] <- t
   }
 
   # Integer or double?

tests/rowRanks.R

@@ -31,15 +31,17 @@ for (kk in 1:4) {
     cat(sprintf("ties.method = %s\n", ties))
     # rowRanks():
     y1 <- matrixStats::rowRanks(x, ties.method = ties)
-    y2 <- t(apply(x, MARGIN = 1L, FUN = rank, na.last = "keep", ties.method = ties))
+    y2 <- t(apply(x, MARGIN = 1L, FUN = rank, na.last = "keep",
+                  ties.method = ties))
     stopifnot(identical(y1, y2))
 
     y3 <- matrixStats::colRanks(t(x), ties.method = ties)
     stopifnot(identical(y1, y3))
 
     # colRanks():
     y1 <- matrixStats::colRanks(x, ties.method = ties)
-    y2 <- t(apply(x, MARGIN = 2L, FUN = rank, na.last = "keep", ties.method = ties))
+    y2 <- t(apply(x, MARGIN = 2L, FUN = rank, na.last = "keep",
+                  ties.method = ties))
     stopifnot(identical(y1, y2))
 
     y3 <- matrixStats::rowRanks(t(x), ties.method = ties)

tests/rowWeightedMedians.R

@@ -51,7 +51,7 @@ stopifnot(all.equal(xM2, xM1))
 
 
 # Weighted row medians with missing values
-xM0 <- apply(x, MARGIN = 1, FUN = weightedMedian, w = w, na.rm = TRUE)
+xM0 <- apply(x, MARGIN = 1L, FUN = weightedMedian, w = w, na.rm = TRUE)
 print(xM0)
 xM1 <- rowWeightedMedians(x, w = w, na.rm = TRUE)
 print(xM1)

tests/sumOver.R

@@ -27,7 +27,8 @@ for (kk in 1:20) {
     cat("Adding NAs\n")
     nna <- sample(n, size = 1L)
     naValues <- c(NA_real_, NaN)
-    x[sample(length(x), size = nna)] <- sample(naValues, size = nna, replace = TRUE)
+    t <- sample(naValues, size = nna, replace = TRUE)
+    x[sample(length(x), size = nna)] <- t
   }
 
   # Integer or double?

tests/sumOver_subset.R

@@ -7,6 +7,10 @@ source("utils/validateIndicesFramework.R")
 x <- runif(6, min = -6, max = 6)
 storage.mode(x) <- "integer"
 for (idxs in indexCases) {
-  validateIndicesTestVector(x, idxs, ftest = sumOver, fsure = sum, na.rm = FALSE)
-  validateIndicesTestVector(x, idxs, ftest = sumOver, fsure = sum, na.rm = TRUE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = sumOver, fsure = sum,
+                            na.rm = FALSE)
+  validateIndicesTestVector(x, idxs,
+                            ftest = sumOver, fsure = sum,
+                            na.rm = TRUE)
 }