Fix CRAN NOTE on Debian system about tests taking too long.

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 0.4.7
-Date: 2024-12-30 15:21:59 UTC
-SHA: 413070797af3a5cf94fd1c7bb7bfe08227d138b8
+Date: 2025-01-07 21:48:22 UTC
+SHA: 099855690ae05afaf95090f4bc9645fa2c0b9246

NEWS.md

@@ -18,6 +18,8 @@
 
 -   Updated CITATION file due to deprecated function and typo.
 
+-   Wrapped a bunch of examples from being run on CRAN submission to avoid Debian system NOTE.
+
 # joineRML 0.4.6
 
 ## Housekeeping

R/confint.mjoint.R

@@ -44,6 +44,7 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' # Fit a classical univariate joint model with a single longitudinal outcome
 #' # and a single time-to-event outcome
 #'
@@ -66,6 +67,7 @@
 #'     control = list(nMCscale = 2, burnin = 5)) # controls for illustration only
 #'
 #' confint(fit1, parm = "Longitudinal")
+#' }
 #'
 #' \dontrun{
 #' # Fit a joint model with bivariate longitudinal outcomes

R/fixef.mjoint.R

@@ -27,6 +27,7 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' # Fit a classical univariate joint model with a single longitudinal outcome
 #' # and a single time-to-event outcome
 #'
@@ -43,6 +44,7 @@
 #'
 #' fixef(fit1, process = "Longitudinal")
 #' fixef(fit1, process = "Event")
+#' }
 #'
 #' \dontrun{
 #' # Fit a joint model with bivariate longitudinal outcomes

R/mjoint.R

@@ -264,6 +264,7 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' # Fit a classical univariate joint model with a single longitudinal outcome
 #' # and a single time-to-event outcome
 #'
@@ -278,6 +279,7 @@
 #'     timeVar = "time",
 #'     control = list(nMCscale = 2, burnin = 5)) # controls for illustration only
 #' summary(fit1)
+#' }
 #'
 #' \dontrun{
 #' # Fit a joint model with bivariate longitudinal outcomes

R/plot.mjoint.R

@@ -16,6 +16,7 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' # Fit a classical univariate joint model with a single longitudinal outcome
 #' # and a single time-to-event outcome
 #'
@@ -32,6 +33,7 @@
 #'
 #' plot(fit1, param = "beta")  # LMM fixed effect parameters
 #' plot(fit1, param = "gamma") # event model parameters
+#' }
 #'
 #' \dontrun{
 #' # Fit a joint model with bivariate longitudinal outcomes

R/vcov.mjoint.R

@@ -41,6 +41,7 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' # Fit a classical univariate joint model with a single longitudinal outcome
 #' # and a single time-to-event outcome
 #'
@@ -56,6 +57,7 @@
 #'     control = list(nMCscale = 2, burnin = 5)) # controls for illustration only
 #'
 #' vcov(fit1)
+#' }
 #'
 #' \dontrun{
 #' # Fit a joint model with bivariate longitudinal outcomes

cran-comments.md

@@ -1,6 +1,7 @@
 ## Other notes
 
-Addresses all NOTES from CRAN Package Check Results.
+* Addresses all NOTES from CRAN Package Check Results.
+* I have stopped several examples from running in order to avoid the NOTE on the Debian system. I cannot reproduce these, but am happy to wrap in `\dontrun{}` blocks.
 
 ## Test environments
 
@@ -13,10 +14,12 @@ Addresses all NOTES from CRAN Package Check Results.
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 notes
+0 errors | 0 warnings | 2 notes
 
 Win-Builder NOTE: "checking CRAN incoming feasibility ... NOTE"
 
+Debian NOTE: "Re-building vignettes had CPU time 5.5 times elapsed time" -- I cannot reproduce this. It passes every other platform. I suspect the qpdf compression tool is the cause, but that was requested by CMD tests.
+
 ## Reverse dependencies
 
 We checked 3 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.