A few fixes to warnings/errors reported by R CMD check.

.Rbuildignore

@@ -1,2 +1,6 @@
 ^docs$
 ^_pkgdown\.yml$
+^\.github$
+^\.circleci$
+^\.travis\.yml$
+^appveyor\.yml$

DESCRIPTION

@@ -1,7 +1,7 @@
 Encoding: UTF-8
 Type: Package
 Package: mr.mash.alpha
-Version: 0.2-28
+Version: 0.2-29
 Date: 2023-08-17
 Title: Multiple Regression with Multivariate Adaptive Shrinkage
 Description: Provides an implementation of methods for multivariate 
@@ -26,11 +26,14 @@ Imports:
     parallel
 Suggests:
     testthat,
-    varbvs
+    varbvs,
+    knitr,
+    rmarkdown,
 LinkingTo:
     Rcpp,
     RcppArmadillo (>= 0.10.4.0.0),
     RcppParallel
+VignetteBuilder: knitr
 Remotes: 
     stephenslab/ebnm,
     stephenslab/mashr,

NAMESPACE

@@ -33,7 +33,9 @@ importFrom(mvtnorm,rmvnorm)
 importFrom(parallel,makeCluster)
 importFrom(parallel,parLapply)
 importFrom(parallel,stopCluster)
+importFrom(stats,coef)
 importFrom(stats,cov)
 importFrom(stats,cov2cor)
 importFrom(stats,lm)
+importFrom(stats,predict)
 useDynLib(mr.mash.alpha)

R/compute_covs.R

@@ -327,6 +327,8 @@ compute_cov_canonical <- function(ntraits, singletons, hetgrid, grid, zeromat=TR
   return(U)
 }
 ###Compute univariate summary statistics
+#
+#' @importFrom stats coef
 get_univariate_sumstats <- function(X, Y, standardize=FALSE, standardize.response=FALSE){
   r <- ncol(Y)
   p <- ncol(X)

R/mr_mash_predict.R

@@ -8,6 +8,9 @@
 #' 
 #' @return Matrix of predicted values.
 #'
+#' @importFrom stats predict
+#'
+#' @method predict mr.mash
 #' @export
 #' @export predict.mr.mash
 #' 
@@ -27,8 +30,11 @@ predict.mr.mash <- function(object, newx, ...){
 #' 
 #' @return (p+1) x r matrix of coefficients.
 #' 
-#' @export
+#' @importFrom stats coef
+#' 
+#' @method coef mr.mash
 #' @export coef.mr.mash
+#' @export
 #' 
 coef.mr.mash <- function(object, ...){
   coeffs <- rbind(object$intercept, object$mu1)