Attempt to fix CRAN NOTE on Debian

NEWS.md

@@ -24,6 +24,8 @@
 
 -   Add R-hub workflow to enable checks for platforms not covered already.
 
+-   Vignettes now force `Sys.setenv("OMP_THREAD_LIMIT" = 2)` to get around CRAN CMD changes.
+
 # joineRML 0.4.6
 
 ## Housekeeping

R/bootSE.R

@@ -89,7 +89,7 @@
 #' }
 bootSE <- function(object, nboot = 100, ci = 0.95, use.mle = TRUE,
                    verbose = FALSE, control = list(), progress = TRUE,
-                   ncores = 1, safe.boot = FALSE, ...) {
+                   ncores = 1L, safe.boot = FALSE, ...) {
 
   if (!inherits(object, "mjoint")) {
     stop("Use only with 'mjoint' model objects.\n")
@@ -168,7 +168,7 @@ bootSE <- function(object, nboot = 100, ci = 0.95, use.mle = TRUE,
       }
     }
 
-  if (ncores > 1) {
+  if (ncores >= 1L) {
     ncores.max <- parallel::detectCores()
     if (ncores > ncores.max) {
       ncores <- ncores.max
@@ -185,6 +185,7 @@ bootSE <- function(object, nboot = 100, ci = 0.95, use.mle = TRUE,
     }
     registerDoSEQ()
   } else {
+    doParallel::registerDoParallel(cores = ncores)
     # *** Serial version (incl. progress bar) ***
     out <- list()
     conv.status <- vector(length = nboot)

R/tidiers.R

@@ -44,7 +44,8 @@
 #' # Extract the survival fixed effects with confidence intervals
 #' tidy(fit, ci = TRUE)
 #'
-#' # Extract the survival fixed effects with confidence intervals based on bootstrapped standard errors
+#' # Extract the survival fixed effects with confidence intervals based on 
+#' # bootstrapped standard errors
 #' bSE <- bootSE(fit, nboot = 5, safe.boot = TRUE)
 #' tidy(fit, bootSE = bSE, ci = TRUE)
 #'
@@ -81,8 +82,15 @@
 #'   \code{estimate}, if required}.
 #'
 #' @export
-tidy.mjoint <- function(x, component = "survival", bootSE = NULL, conf.int = FALSE, conf.level = 0.95, ...) {
+tidy.mjoint <- function(x, 
+                        component = "survival", 
+                        bootSE = NULL, 
+                        conf.int = FALSE, 
+                        conf.level = 0.95, 
+                        ...) {
+
   component <- match.arg(component, c("survival", "longitudinal"))
+
   if (!is.null(bootSE)) {
     if (!inherits(x = bootSE, what = "bootSE")) stop("'bootSE' object not of class 'bootSE'")
   }
@@ -121,6 +129,7 @@ tidy.mjoint <- function(x, component = "survival", bootSE = NULL, conf.int = FAL
 
   # return tidy object
   return(out)
+
 }
 
 
@@ -148,6 +157,7 @@ tidy.mjoint <- function(x, component = "survival", bootSE = NULL, conf.int = FAL
 #'
 #' @export
 augment.mjoint <- function(x, data = x$data, ...) {
+
   # checks on 'data'
   if (is.null(data)) {
     stop("It was not possible to extract 'data' from 'x'. Please provide 'data' manually.")
@@ -164,6 +174,7 @@ augment.mjoint <- function(x, data = x$data, ...) {
   fit0 <- fitted(x, level = 0)
   names(fit0) <- paste0(".fitted_", names(fit0), "_0")
   fit0 <- do.call(cbind.data.frame, fit0)
+
   fit1 <- fitted(x, level = 1)
   names(fit1) <- paste0(".fitted_", names(fit1), "_1")
   fit1 <- do.call(cbind.data.frame, fit1)
@@ -180,6 +191,7 @@ augment.mjoint <- function(x, data = x$data, ...) {
   out <- cbind(data, fit0, fit1, res0, res1)
   out <- tibble::as_tibble(out)
   return(out)
+
 }
 
 
@@ -197,6 +209,7 @@ augment.mjoint <- function(x, data = x$data, ...) {
 #'
 #' @export
 glance.mjoint <- function(x, ...) {
+
   smr <- summary(x)
   out <- data.frame(t(smr$sigma))
   out$AIC <- smr$AIC
@@ -205,4 +218,5 @@ glance.mjoint <- function(x, ...) {
   rownames(out) <- NULL
   out <- tibble::as_tibble(out)
   return(out)
+
 }

vignettes/joineRML-tidy.Rmd

@@ -11,14 +11,16 @@ editor_options:
   chunk_output_type: console
 ---
 
-```{r load-joineRML, include = FALSE}
+```{r load-joineRML, include=FALSE}
 library(joineRML)
 library(knitr)
+Sys.setenv("OMP_THREAD_LIMIT" = 2)
 ```
 
 # Introduction
 
 Tidiers for objects of class `mjoint` have been included in latest release of `joineRML` package (0.4.5).
+
 The purpose of these tidiers are described in the introductory vignette to `broom`:
 
 > The broom package takes the messy output of built-in functions in R, such as `lm`, `nls`, or `t.test`, and turns them into tidy data frames.
@@ -37,7 +39,7 @@ These methods are specifically useful when plotting results of a joint model or
 
 We use the sample example from the introductory vignette to `joineRML` using the heart valve data.
 
-```{r vignette, eval = FALSE}
+```{r vignette, eval=FALSE}
 vignette("joineRML", package = "joineRML")
 help("heart.valve", package = "joineRML")
 ```
@@ -55,7 +57,7 @@ Further to that, we only select the first 50 individuals to speed up these examp
 hvd <- hvd[hvd$num <= 50, ]
 ```
 
-```{r hvd_model_fit, cache = TRUE}
+```{r hvd_model_fit, cache=TRUE}
 set.seed(12345)
 fit <- mjoint(
   formLongFixed = list(
@@ -95,7 +97,7 @@ tidy(fit, ci = TRUE, conf.level = 0.99)
 
 The standard errors reported by default are based on the empirical information matrix, as in `mjoint`. It is of course possible to use bootstrapped standard errors as follows:
 
-```{r tidy-boot, eval = FALSE}
+```{r tidy-boot, eval=FALSE}
 bSE <- bootSE(fit, nboot = 100, safe.boot = TRUE, progress = FALSE)
 tidy(fit, boot_se = bSE, conf.int = TRUE)
 ```
@@ -104,7 +106,7 @@ The results of this example are not included as it would take too long to run fo
 
 The `tidy` method is useful for custom plotting (e.g. forest plots) of results from `joineRML` models, all in a tidy framework:
 
-```{r tidy-plotting, fig.height = 5, fig.width = 5, fig.align = "center"}
+```{r tidy-plotting, fig.height=5, fig.width=5, fig.align="center"}
 library(ggplot2)
 out <- tidy(fit, conf.int = TRUE)
 ggplot(out, aes(x = term, y = estimate, ymin = conf.low, ymax = conf.high)) +

vignettes/joineRML.Rmd

@@ -9,7 +9,7 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r, echo = FALSE, message = FALSE}
+```{r, echo=FALSE, message=FALSE}
 #knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
 library(Matrix)
 library(nlme)
@@ -21,6 +21,8 @@ if (requireNamespace('joineR', quietly = TRUE)) {
 } else {
   message("'joineR' not available")
 }
+
+Sys.setenv("OMP_THREAD_LIMIT" = 2)
 ```
 
 # Introduction