doc fix and hdf5r now works with GHA

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

@@ -53,7 +53,17 @@ jobs:
             ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1
             ${{ runner.os }}-${{ hashFiles('.github/R-version') }}
             ${{ runner.os }}-
+
+      - name: Build HDF5 - OSX
+        if: runner.os == 'macOS'
+        run: |
+          brew install hdf5
           
+      - name: Build HDF5 - LINUX
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install -y libhdf5-dev
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)

R/multiscaleSVDxpts.R

@@ -457,7 +457,7 @@ sparseDistanceMatrixXY <- function(x, y, k = 3, r = Inf, sigma = NA,
 #' which eigenvector off which to base the scale of the y-axis.'
 #' @return list with a vector of tangent, curvature, noise dimensionality and a
 #' a dataframe containing eigenvalues across scale, in correspondence with r:
-#' \itemize{
+#' \describe{
 #'   \item{dim: }{The tangent, curvature and noise dimensionality vector.  The
 #' data dimensionality is the first entry, the curvature dimensionality exists
 #' from the second to the first entry of the noise vector.}
@@ -1572,8 +1572,7 @@ jointSmoothMatrixReconstruction <- function(
 #' set.seed(123)
 #' m <- matrix(rnorm(500), nrow = 5)
 #' result <- optimize_indicator_matrix(m, max_iter = 1000, tol = 1e-6, verbose = TRUE)
-#' print(result$I)
-#' print(result$objective_value)
+#' print(result)
 #' @export
 optimize_indicator_matrix <- function(m, max_iter = 1000, tol = 1e-6, preprocess = TRUE, verbose = FALSE) {
   if (preprocess) {

R/rftResults.R

@@ -38,7 +38,7 @@
 #'
 #' @return Outputs a statistical value to be used for threshTypeold a
 #' statistical field image
-#' \descrbie{
+#' \describe{
 #' \item{SetStats: }{set-level statistics and number of clusters}
 #' \item{ClusterStats: }{cluster-level statistics and descriptors}
 #' \item{PeakStats: }{peak-level statistics and descriptor"}

R/zzz_Summary.R

@@ -153,15 +153,15 @@ useAsDefault = .all_def, group = "Summary"
 )
 
 
-#' #' @rdname antsImagemath
-#' #' @aliases xor,antsImage-method
-#' setMethod(f = "xor", signature(x = "antsImage",
-#'                              y = "antsImage"), definition = function(x) {
-#'   xx = as.array(x)
-#'   yy = as.array(y)
-#'   xor(xx, yy)
-#'   !a2
-#' })
+# # @rdname antsImagemath
+# # @aliases xor,antsImage-method
+# setMethod(f = "xor", signature(x = "antsImage",
+#                              y = "antsImage"), definition = function(x) {
+#   xx = as.array(x)
+#   yy = as.array(y)
+#   xor(xx, yy)
+#   !a2
+# })
 
 
 #' @title Mean for antsImage Objects