Removed long-running examples (or added \dontrun).

Author: pcarbo

DESCRIPTION

@@ -2,7 +2,7 @@ Package: mashr
 Type: Package
 Encoding: UTF-8
 Title: Multivariate Adaptive Shrinkage 
-Version: 0.2.76
+Version: 0.2.77
 Date: 2023-10-17
 Authors@R: c(person("Matthew","Stephens",role="aut"),
              person("Sarah","Urbut",role="aut"),

R/data2cov.R

@@ -183,11 +183,13 @@ cov_flash = function (data, factors = c("default","nonneg"),
 #' matrices. It can be initialized with, for example running \code{cov_pca} with,
 #' say, 5 PCs.
 #' @examples
+#' \dontrun{
 #' data = mash_set_data(Bhat = cbind(c(1,2),c(3,4)), Shat = cbind(c(1,1),c(1,1)))
 #' U_pca = cov_pca(data,2)
 #' U_x = apply(data$Bhat, 2, function(x) x - mean(x))
 #' U_xx = t(U_x) %*% U_x / nrow(U_x)
 #' cov_ed(data,c(U_pca, list(xx = U_xx)))
+#' }
 #'
 #' @export
 #'

R/extreme_deconvolution.R

@@ -88,6 +88,7 @@
 #' Roweis, Submitted to AOAS (2009) [arXiv/0905.2979]
 #' 
 #' @examples
+#' \dontrun{
 #' ydata <-
 #' c(2.62434536, 0.38824359, 0.47182825, -0.07296862, 1.86540763,
 #'   -1.30153870, 2.74481176, 0.23879310, 1.31903910, 0.75062962,
@@ -143,6 +144,7 @@
 #'   projection[[i]] = matrix(c(i%%2,(i+1)%%2),1,2)
 #' res <- extreme_deconvolution(ydata, ycovar, xamp, xmean, xcovar,
 #'          projection=projection, logfile="ExDeconDemo")
+#' }
 #' 
 #' @export
 #' 

R/get_functions.R

@@ -113,11 +113,6 @@ get_n_significant_conditions = function(m, thresh = 0.05, conditions = NULL,
 #'
 #' @importFrom ashr get_fitted_g
 #'
-#' @examples
-#' simdata = simple_sims(50,5,1)
-#' data = mash_set_data(simdata$Bhat, simdata$Shat)
-#' m = mash(data, cov_canonical(data))
-#' get_estimated_pi(m)
 #' @export
 #'
 get_estimated_pi = function(m, dimension = c("cov","grid","all")){
@@ -274,4 +269,4 @@ get_pairwise_sharing_from_samples = function(m, factor=0.5, lfsr_thresh=0.05, FU
 
 get_ncond = function(m){
   return(ncol(get_pm(m)))
-}
+}