omp thread limit

helske · Oct 24, 2023 · 3b5c6c1 · 3b5c6c1
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diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-bssm 2.0.2 (Release date: 2023-09-04)
+bssm 2.0.2 (Release date: 2023-10-18)
 =====================================
    * Switched to markdown NEWS with a plan to be more clear about the future
      changes in the package.
@@ -11,6 +11,8 @@ bssm 2.0.2 (Release date: 2023-09-04)
    * Removed explicit C++ version requirement as required by new CRAN policies.
    * Removed `magrittr` dependency and switched to native pipe, leading to 
      requirement for R 4.1.0+.
+   * Added Sys.setenv("OMP_THREAD_LIMIT" = 2) to fix weird CRAN issues with 
+     parallelisation on Debian.
 
 bssm 2.0.1 (Release date: 2022-05-02)
 ==============

diff --git a/R/approx.R b/R/approx.R
@@ -31,6 +31,7 @@
 #' @export
 #' @rdname gaussian_approx
 #' @examples 
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' data("poisson_series")
 #' model <- bsm_ng(y = poisson_series, sd_slope = 0.01, sd_level = 0.1,
 #'   distribution = "poisson")

diff --git a/R/bssm-package.R b/R/bssm-package.R
@@ -89,6 +89,7 @@
 #' time ts ts.union tsp tsp<- sd na.omit
 #' @useDynLib bssm
 #' @examples
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' # Create a local level model (latent random walk + noise) to the Nile
 #' # dataset using the bsm_lg function:
 #' model <- bsm_lg(Nile,
@@ -138,6 +139,7 @@ NULL
 #' \url{https://stat.fi/tup/tilastotietokannat/index_en.html}.
 #' @keywords datasets
 #' @examples
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' data("drownings")
 #' model <- bsm_ng(drownings[, "deaths"], u = drownings[, "population"],
 #'   xreg = drownings[, "summer_temp"], distribution = "poisson",
@@ -165,6 +167,7 @@ NULL
 #' Time Series Analysis by State Space Methods. Oxford University Press.
 #' https://doi.org/10.1093/acprof:oso/9780199641178.001.0001
 #' @examples
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' data("exchange")
 #' model <- svm(exchange, rho = uniform(0.97,-0.999,0.999),
 #'  sd_ar = halfnormal(0.175, 2), mu = normal(-0.87, 0, 2))
@@ -188,6 +191,7 @@ NULL
 #' Scand J Statist. 1-38. https://doi.org/10.1111/sjos.12492
 #'
 #' @examples
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' # The data was generated as follows:
 #' set.seed(321)
 #' slope <- cumsum(c(0, rnorm(99, sd = 0.01)))
@@ -241,6 +245,7 @@ NULL
 #' https://doi.org/10.32614/RJ-2021-103
 #'
 #' @examples
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' # reproducing the model:
 #' data("negbin_series")
 #' # Construct model for bssm

diff --git a/R/ekpf_filter.R b/R/ekpf_filter.R
@@ -21,6 +21,7 @@ ekpf_filter <- function(model, particles, ...) {
 #' @rdname ekpf_filter
 #' @examples
 #' \donttest{ # Takes a while
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' set.seed(1)
 #' n <- 50
 #' x <- y <- numeric(n)

diff --git a/R/kfilter.R b/R/kfilter.R
@@ -69,6 +69,7 @@ kfilter.nongaussian <- function(model, ...) {
 #' @export
 #' @examples
 #' \donttest{ # Takes a while on CRAN
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' set.seed(1)
 #' mu <- -0.2
 #' rho <- 0.7
@@ -138,6 +139,7 @@ ekf <- function(model, iekf_iter = 0) {
 #' @export
 #' @examples
 #' \donttest{ # Takes a while on CRAN
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' set.seed(1)
 #' mu <- -0.2
 #' rho <- 0.7

diff --git a/R/models.R b/R/models.R
@@ -61,6 +61,7 @@ default_update_fn <- function(theta) {
 #' @return An object of class \code{ssm_ulg}.
 #' @export
 #' @examples 
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' 
 #' # Regression model with time-varying coefficients
 #' set.seed(1)

diff --git a/R/post_correction.R b/R/post_correction.R
@@ -174,6 +174,7 @@ suggest_N <- function(model, theta,
 #' @export
 #' @examples 
 #' \donttest{
+#' Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 #' set.seed(1)
 #' n <- 300
 #' x1 <- sin((2 * pi / 12) * 1:n)

diff --git a/man/bssm.Rd b/man/bssm.Rd
diff --git a/man/drownings.Rd b/man/drownings.Rd
diff --git a/man/ekf.Rd b/man/ekf.Rd
diff --git a/man/ekpf_filter.Rd b/man/ekpf_filter.Rd
diff --git a/man/exchange.Rd b/man/exchange.Rd
diff --git a/man/gaussian_approx.Rd b/man/gaussian_approx.Rd
diff --git a/man/negbin_model.Rd b/man/negbin_model.Rd
diff --git a/man/poisson_series.Rd b/man/poisson_series.Rd
diff --git a/man/post_correct.Rd b/man/post_correct.Rd
diff --git a/man/ssm_ulg.Rd b/man/ssm_ulg.Rd
diff --git a/man/ukf.Rd b/man/ukf.Rd
diff --git a/tests/test_all.R b/tests/test_all.R
@@ -1,2 +1,4 @@
+Sys.setenv("OMP_THREAD_LIMIT" = 2)
+
 library("testthat")
 test_check("bssm")
diff --git a/vignettes/bssm.Rmd b/vignettes/bssm.Rmd
@@ -14,6 +14,7 @@ vignette: |
 ---
 
 ```{r, echo = FALSE}
+Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 if (!requireNamespace("rmarkdown") ||
     !rmarkdown::pandoc_available("1.12.3")) {
   warning(call. = FALSE, "These vignettes assume rmarkdown and pandoc version",

diff --git a/vignettes/growth_model.Rmd b/vignettes/growth_model.Rmd
@@ -14,6 +14,7 @@ vignette: |
 ---
 
 ```{r, echo = FALSE}
+Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 if (!requireNamespace("rmarkdown") ||
     !rmarkdown::pandoc_available("1.12.3")) {
   warning(call. = FALSE, "These vignettes assume rmarkdown and pandoc version 1.12.3. These were not found. Older versions will not work.")

diff --git a/vignettes/psi_pf.Rmd b/vignettes/psi_pf.Rmd
@@ -16,6 +16,7 @@ bvignette: |
 ```
 
 ```{r, echo = FALSE}
+Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 if (!requireNamespace("rmarkdown") ||
     !rmarkdown::pandoc_available("1.12.3")) {
   warning(call. = FALSE, "These vignettes assume rmarkdown and pandoc version 1.12.3. These were not found. Older versions will not work.")

diff --git a/vignettes/sde_model.Rmd b/vignettes/sde_model.Rmd
@@ -14,6 +14,7 @@ vignette: |
 ---
 
 ```{r, echo = FALSE}
+Sys.setenv("OMP_THREAD_LIMIT" = 2) # For CRAN
 if (!requireNamespace("rmarkdown") ||
     !rmarkdown::pandoc_available("1.12.3")) {
   warning(call. = FALSE, "These vignettes assume rmarkdown and pandoc version 1.12.3. These were not found. Older versions will not work.")