ENH: reduce unused or rarely used dependencies

.github/workflows/R-CMD-check.yaml

@@ -1,8 +1,8 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
-  schedule:
-    - cron: '0 0 * * *'
+  pull_request:
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -21,6 +21,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
 
     steps:
       - uses: actions/checkout@v4
@@ -33,10 +34,29 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v3
         with:
-          extra-packages: any::rcmdcheck
-          needs: check
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1
+          restore-keys: |
+            ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1
+            ${{ runner.os }}-${{ hashFiles('.github/R-version') }}
+            ${{ runner.os }}-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:

DESCRIPTION

@@ -5,11 +5,11 @@ Version: 0.6.0
 Date: 2024-03-23
 Authors@R: c(
     person(c("Brian", "B"), "Avants", role = c("aut", "cre"), email = "stnava@gmail.com"),
-    person(c("Benjamin", "M"), "Kandel", role = "ctb", email = "NA"),
-    person(c("Jeff", "T"), "Duda", role = "ctb", email = "NA"),
-    person(c("Philip", "A"), "Cook", role = "ctb", email = "NA"),
-    person(c("Nicholas", "J"), "Tustison", role = "ctb", email = "NA"),
-    person(c("Dorian"), "Pustina", role = "ctb", email = "NA")
+    person(c("Benjamin", "M"), "Kandel", role = "ctb"),
+    person(c("Jeff", "T"), "Duda", role = "ctb"),
+    person(c("Philip", "A"), "Cook", role = "ctb"),
+    person(c("Nicholas", "J"), "Tustison", role = "ctb"),
+    person(c("Dorian"), "Pustina", role = "ctb")
     )
 Maintainer: Brian B. Avants <stnava@gmail.com>
 Description: ANTsR interfaces state of the art image processing with R
@@ -33,8 +33,8 @@ Imports:
     stats,
     utils
 Suggests:
+    colormap,
     magic,
-    psych,
     rsvd,
     abind,
     BGLR,
@@ -43,12 +43,10 @@ Suggests:
     corpcor,
     dplyr,
     e1071,
-    extremevalues,
     fastICA,
     fpc,
     ggplot2,
     glasso,
-    glmnet,
     grid,
     hdf5r,
     igraph,
@@ -57,14 +55,11 @@ Suggests:
     MASS,
     Matrix,
     mFilter,
-    misc3d,
     moments,
-    networkD3,
     pixmap,
     png,
     pracma,
     randomForest,
-    R.matlab,
     RcppEigen,
     RcppHNSW,
     rgl,
@@ -76,7 +71,6 @@ Suggests:
     testthat,
     tools,
     viridis,
-    visreg,
     xgboost,
     FNN
 LazyData: TRUE

NAMESPACE

@@ -124,6 +124,7 @@ export(combineNuisancePredictors)
 export(compcor)
 export(components)
 export(composeAntsrTransforms)
+export(composeDisplacementFields)
 export(composeTransformsToField)
 export(computeDVARS)
 export(computeDVARSspatialMap)
@@ -279,11 +280,8 @@ export(readNormalizedPopulationData)
 export(reflectImage)
 export(reflectionMatrix)
 export(regressProjections)
-export(regressionNetworkViz)
 export(regularizeSimlr)
 export(reho)
-export(renderImageLabels)
-export(renderSurfaceFunction)
 export(renormalizeProbabilityImages)
 export(reorientImage)
 export(resampleImage)
@@ -398,9 +396,12 @@ exportMethods(tan)
 exportMethods(tanh)
 exportMethods(tanpi)
 exportMethods(trunc)
+import(ANTsRCore)
+import(grDevices)
 import(methods)
 import(stats)
 import(tools)
+import(utils)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,dev.new)
 importFrom(grDevices,dev.off)
@@ -426,60 +427,4 @@ importFrom(graphics,title)
 importFrom(magrittr,"%>%")
 importFrom(methods,is)
 importFrom(methods,new)
-importFrom(stats,ar)
-importFrom(stats,as.formula)
-importFrom(stats,chisq.test)
-importFrom(stats,coefficients)
-importFrom(stats,convolve)
-importFrom(stats,cor)
-importFrom(stats,cor.test)
-importFrom(stats,cov)
-importFrom(stats,density)
-importFrom(stats,dist)
-importFrom(stats,dnorm)
-importFrom(stats,formula)
-importFrom(stats,glm)
-importFrom(stats,lm)
-importFrom(stats,lm.fit)
-importFrom(stats,loess)
-importFrom(stats,median)
-importFrom(stats,model.frame)
-importFrom(stats,model.matrix)
-importFrom(stats,model.response)
-importFrom(stats,na.omit)
-importFrom(stats,optim)
-importFrom(stats,optimize)
-importFrom(stats,p.adjust)
-importFrom(stats,pchisq)
-importFrom(stats,pf)
-importFrom(stats,pnorm)
-importFrom(stats,ppois)
-importFrom(stats,prcomp)
-importFrom(stats,predict)
-importFrom(stats,pt)
-importFrom(stats,qchisq)
-importFrom(stats,qf)
-importFrom(stats,qnorm)
-importFrom(stats,qt)
-importFrom(stats,quantile)
-importFrom(stats,residuals)
-importFrom(stats,rnorm)
-importFrom(stats,sd)
-importFrom(stats,spec.pgram)
-importFrom(stats,spline)
-importFrom(stats,stl)
-importFrom(stats,t.test)
-importFrom(stats,toeplitz)
-importFrom(stats,ts)
-importFrom(stats,var)
-importFrom(utils,capture.output)
-importFrom(utils,data)
-importFrom(utils,download.file)
-importFrom(utils,glob2rx)
-importFrom(utils,install.packages)
-importFrom(utils,read.csv)
-importFrom(utils,setTxtProgressBar)
-importFrom(utils,tail)
-importFrom(utils,txtProgressBar)
-importFrom(utils,unzip)
-importFrom(utils,write.csv)
+importFrom(stats,AIC)

R/ANTsR-package.R

@@ -0,0 +1,14 @@
+#' @title Advanced Normalization Tools in R
+#' @name ANTsR
+#'
+#' @importFrom stats AIC
+#'
+#' @import ANTsRCore stats grDevices utils
+#'
+#' @keywords internal
+"_PACKAGE"
+# The following block is used by usethis to automatically manage
+# roxygen namespace tags. Modify with care!
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/abpBrainExtraction.R

@@ -20,9 +20,6 @@
 #' @return outputs a brain image and brain mask.
 #' @author Tustison N, Avants BB
 #' @examples
-#'
-#' Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = 1)
-#' set.seed(1)
 #' n <- 64
 #' fn <- getANTsRData("r16")
 #' img <- antsImageRead(fn)
@@ -33,25 +30,10 @@
 #' temmask <- antsImageClone(tem)
 #' temmask[tem > 20] <- 1
 #' temmask[tem <= 20] <- 0
-#' bm <- ANTsR::abpBrainExtraction(img = img, tem = tem, temmask = temmask, num_threads = 1)
-#' stopifnot(sum(bm$bmask) != prod(dim(bm$brain)))
-#' bm2 <- ANTsR::abpBrainExtraction(img = img, tem = tem, temmask = temmask, num_threads = 1)
-#' stopifnot(sum(bm2$bmask) != prod(dim(bm2$brain)))
-#'
+#' \dontrun{
+#' bm <- abpBrainExtraction(img = img, tem = tem, temmask = temmask)
+#' }
 #' @export abpBrainExtraction
-#' @importFrom magrittr %>%
-#' @importFrom graphics hist par plot points
-#' @importFrom grDevices colorRampPalette dev.off hsv png rainbow rgb
-#' @importFrom methods new
-#' @importFrom stats ar as.formula coefficients convolve
-#'   cor cor.test cov dist formula glm lm
-#'   lm.fit loess median model.matrix na.omit
-#'   optimize p.adjust pchisq pf pnorm ppois
-#'   predict pt qchisq qf qnorm qt quantile
-#'   residuals rnorm sd spec.pgram spline stl
-#'   t.test toeplitz ts var
-#' @importFrom utils data glob2rx read.csv setTxtProgressBar tail
-#'   txtProgressBar write.csv
 abpBrainExtraction <- function(img, tem, temmask,
                                temregmask = NULL, regtype = "SyN", tdir = NA,
                                num_threads = 1,

R/abpN4.R

@@ -24,7 +24,7 @@ abpN4 <- function(
     mask, usen3 = FALSE,
     ...) {
   numargs <- nargs()
-  if (numargs < 1 | missing(img) | class(img)[1] != "antsImage") {
+  if (numargs < 1 | missing(img) | !inherits(img, "antsImage")) {
     stop("Missing image.")
   }
   if (length(intensityTruncation) != 3) {

R/antsAffineInitializer.R

@@ -31,17 +31,6 @@
 #' mi2 <- resampleImage(mi, c(1.25, 1.25))
 #' tx <- affineInitializer(fi, mi2)
 #' tx2 <- affineInitializer(fi, mi2)
-#' if ("R.matlab" %in% installed.packages()) {
-#'   tx_hdr <- R.matlab::readMat(tx)
-#'   trans <- tx_hdr$AffineTransform.double.2.2
-#'   fixed <- tx_hdr$fixed
-#'
-#'   tx2_hdr <- R.matlab::readMat(tx2)
-#'   trans2 <- tx2_hdr$AffineTransform.double.2.2
-#'   fixed2 <- tx2_hdr$fixed
-#'
-#'   testthat::expect_equal(tx_hdr, tx2_hdr)
-#' }
 #'
 #' @export affineInitializer
 affineInitializer <- function(

R/antsApplyTransformsToPoints.R

@@ -28,7 +28,7 @@
 #' moving <- resampleImage(moving, c(64, 64), 1, 0)
 #' mytx <- antsRegistration(
 #'   fixed = fixed, moving = moving,
-#'   typeofTransform = c("SyN"), verbose = TRUE
+#'   typeofTransform = c("SyN"), verbose = FALSE
 #' )
 #' pts <- data.frame(
 #'   x = c(110.5, 120, 130), y = c(108.1, 121.0, 130),
@@ -104,7 +104,7 @@ antsApplyTransformsToPoints <- function(
         )
       }
     }
-    if (class(points)[[1]] != "antsImage") {
+    if (!inherits(points, "antsImage")) {
       usepts <- as.antsImage(data.matrix(points))
     } else {
       usepts <- antsImageClone(points)
@@ -125,7 +125,7 @@ antsApplyTransformsToPoints <- function(
     }
     ANTsRCore::antsApplyTransformsToPoints(c(myargs, "-f", 1, "--precision", 0))
 
-    if (class(points)[[1]] == "antsImage") {
+    if (inherits(points, "antsImage")) {
       return(pointsout)
     }
     pointsout <- data.frame(as.matrix(pointsout))

R/antsAverageImages.R

@@ -27,7 +27,7 @@ antsAverageImages <- function(imageList, normalize = FALSE, weights,
                               verbose = TRUE) {
   # determine if input is list of images or filenames
   isfile <- FALSE
-  if (class(imageList) == "character") {
+  if (inherits(imageList, "character")) {
     if (any(!file.exists(imageList))) {
       stop("One or more files do not exist.")
     }

R/antsBOLDNetworkAnalysis.R

@@ -55,7 +55,6 @@ antsBOLDNetworkAnalysis <- function(
     }
     return(x)
   }
-  # if ( !usePkg("psych") ) { print("Need pysch package"); return(NULL) }
   # if ( !usePkg("glasso") ) { print("Need glasso package"); return(NULL) }
   # if ( !usePkg("igraph") ) { print("Need igraph package"); return(NULL) }
   stopifnot(!is.null(bold))
@@ -133,9 +132,6 @@ antsBOLDNetworkAnalysis <- function(
     bgdnuis <- bgsvd$u[, 1:newnuisv]
     colnames(bgdnuis) <- paste("bgdNuis", 1:newnuisv, sep = "")
   }
-  if (winsortrim > 0) {
-    omat <- psych::winsor(omat, trim = winsortrim)
-  }
   omat <- omat[keepinds, ]
   ##################################################
   classiccompcor <- compcor(omat, mask = mask, ncompcor = 4)

R/antsCopyImageInfo.R

@@ -17,7 +17,7 @@
 antsCopyImageInfo <- function(reference, target) {
   reference <- check_ants(reference)
   target <- check_ants(target)
-  if (!(class(reference) == "antsImage") || !(class(target) == "antsImage")) {
+  if (!(inherits(reference, "antsImage")) || !(inherits(target, "antsImage"))) {
     stop("Both inputs must be of class 'antsImage'")
   }
   antsSetOrigin(target, as.numeric(antsGetOrigin(reference)))
@@ -47,7 +47,7 @@ antsCopyImageInfo <- function(reference, target) {
 antsCopyImageInfo2 <- function(target, reference) {
   reference <- check_ants(reference)
   target <- check_ants(target)
-  if (!(class(reference) == "antsImage") || !(class(target) == "antsImage")) {
+  if (!(inherits(reference, "antsImage")) || !(inherits(target, "antsImage"))) {
     stop("Both inputs must be of class 'antsImage'")
   }
   antsSetOrigin(target, as.numeric(antsGetOrigin(reference)))

R/antsImageRead.R

@@ -23,16 +23,16 @@
 antsImageRead <- function(filename, dimension = NULL, pixeltype = "float") {
   components <- 1
 
-  if (class(filename) != "character" || length(filename) != 1) {
+  if (!is.character(filename) || length(filename) != 1) {
     stop("'filename' argument must be of class 'character' and have length 1")
   }
   filename <- path.expand(filename)
   if (!file.exists(filename)) stop("file does not exist")
-  if (class(pixeltype) != "character" || length(pixeltype) != 1) {
+  if (!is.character(pixeltype) || length(pixeltype) != 1) {
     stop("'pixeltype' argument must be of class 'character' and have length 1")
   }
   if (!is.null(dimension)) {
-    if (((class(dimension) != "numeric") && (class(dimension) != "integer")) || length(dimension) !=
+    if (((!is.numeric(dimension)) && (!is.integer(dimension))) || length(dimension) !=
       1) {
       stop("'dimension' argument must be of class 'numeric' and have length 1")
     }