solaris bug fix

USEPA · Oct 19, 2021 · 9d03e4e · 9d03e4e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: spsurvey
 Title: Spatial Sampling Design and Analysis
-Version: 5.0.0
+Version: 5.0.1
 Authors@R: c(
     person("Michael", "Dumelle", role=c("aut","cre"),
            email = "[email protected]", comment = c(ORCID = "0000-0002-3393-5529")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# spsurvey 5.0.1 (2021-10-18)
+
+## Bug fix
+
+* Addressed Solaris performance problems.
+
 # spsurvey 5.0.0 (2021-10-15)
 
 ## Major Updates

diff --git a/R/dsgn_check.R b/R/dsgn_check.R
@@ -347,20 +347,20 @@ dsgn_check <- function(sframe, sf_type, legacy_sites, legacy_option, stratum, se
       if (is.list(n_over)) {
         if (any(sapply(stratum, function(x) (n_base[[x]] + ifelse(is.null(n_over[[x]]), 0, sum(n_over[[x]]))) > NROW(sframe[sframe[[stratum_var]] == x, , drop = FALSE])))) {
           stop_ind <- TRUE
-          stop_mess <- paste0("For each stratum, the sum of the base sites and 'Over' replacement sites must be no larger than the number of rows in 'sframe' representing that stratum")
+          stop_mess <- paste0("For each stratum, the sum of the base sites and 'Over' replacement sites must be no larger than the number of rows in 'sframe' representing that stratum.")
           stop_df <- rbind(stop_df, data.frame(func = I("n_base + n_over"), I(stop_mess)))
         }
       } else {
         if (any(sapply(stratum, function(x) (n_base[[x]] + sum(n_over)) > NROW(sframe[sframe[[stratum_var]] == x, , drop = FALSE])))) {
           stop_ind <- TRUE
-          stop_mess <- paste0("For each stratum, the sum of the base sites and 'Over' replacement sites must be no larger than the number of rows in 'sframe' representing that stratum")
+          stop_mess <- paste0("For each stratum, the sum of the base sites and 'Over' replacement sites must be no larger than the number of rows in 'sframe' representing that stratum.")
           stop_df <- rbind(stop_df, data.frame(func = I("n_base + n_over"), I(stop_mess)))
         }
       }
     } else {
       if ((n_base + sum(n_over)) > NROW(sframe)) {
         stop_ind <- TRUE
-        stop_mess <- paste0("The sum of the base sites and 'Over' replacement sites must be no larger than the number of rows in 'sframe'")
+        stop_mess <- paste0("The sum of the base sites and 'Over' replacement sites must be no larger than the number of rows in 'sframe'.")
         stop_df <- rbind(stop_df, data.frame(func = I("n_base + n_over"), I(stop_mess)))
       }
     }
@@ -375,6 +375,14 @@ dsgn_check <- function(sframe, sf_type, legacy_sites, legacy_option, stratum, se
     }
   }
 
+  # find system info
+  on_solaris <- Sys.info()[["sysname"]] == "SunOS"
+  if (on_solaris) {
+    stop_ind <- TRUE
+    stop_mess <- paste0("grts() and irs() are not supported on Solaris.")
+    stop_df <- rbind(stop_df, data.frame(func = I("Solaris"), I(stop_mess)))
+  }
+
   ### If any issues, write out stop_df and then stop
   if (stop_ind) {
     names(stop_df) <- c("Design Input", "Error Message")

diff --git a/R/grts.R b/R/grts.R
@@ -274,10 +274,12 @@
 #' of natural resources. \emph{Journal of the american Statistical association}, 99(465), 262-278.
 #'
 #' @examples
+#' \dontrun{
 #' sample <- grts(NE_Lakes, n_base = 100)
 #' strata_n <- c(low = 25, high = 30)
 #' sample_strat <- grts(NE_Lakes, n_base = strata_n, stratum_var = "ELEV_CAT")
 #' sample_over <- grts(NE_Lakes, n_base = 30, n_over = 5)
+#' }
 #' @export
 ################################################################################
 grts <- function(sframe, n_base, stratum_var = NULL, seltype = NULL, caty_var = NULL,

diff --git a/R/irs.R b/R/irs.R
@@ -21,13 +21,14 @@
 #'  }
 #'
 #' @examples
+#' \dontrun{
 #' sample <- irs(NE_Lakes, n_base = 100)
 #' strata_n <- c(low = 25, high = 30)
 #' sample_strat <- irs(NE_Lakes, n_base = strata_n, stratum_var = "ELEV_CAT")
 #' sample_over <- irs(NE_Lakes, n_base = 30, n_over = 5)
+#' }
 #' @export
 ###############################################################################
-
 irs <- function(sframe, n_base, stratum_var = NULL, seltype = NULL, caty_var = NULL,
                 caty_n = NULL, aux_var = NULL, legacy_var = NULL,
                 legacy_sites = NULL, legacy_stratum_var = NULL,

diff --git a/R/sp_balance.R b/R/sp_balance.R
@@ -61,16 +61,24 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' sample <- grts(NE_Lakes, 30)
 #' sp_balance(sample$sites_base, NE_Lakes)
 #' strata_n <- c(low = 25, high = 30)
 #' sample_strat <- grts(NE_Lakes, n_base = strata_n, stratum_var = "ELEV_CAT")
 #' sp_balance(sample_strat$sites_base, NE_Lakes, stratum_var = "ELEV_CAT", metric = "rmse")
+#' }
 sp_balance <- function(object, sframe, stratum_var = NULL, ip = NULL, metrics = "pielou", extents = FALSE) {
   if (inherits(object, "spdesign")) {
     stop("object must be an sf object. If object is output from grts() or irs(), instead 1) use object$sites_legacy, object$sites_base, object$sites_over, or object$sites_near; or 2) use sp_rbind().")
   }
 
+  # find system info
+  on_solaris <- Sys.info()[["sysname"]] == "SunOS"
+  if (on_solaris) {
+    stop("sp_balance() is not supported on Solaris.")
+  }
+
   if (is.null(stratum_var)) {
     object$stratum_var <- "None"
     sframe$stratum_var <- "None"

diff --git a/R/sp_plot.R b/R/sp_plot.R
@@ -87,12 +87,14 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' data("NE_Lakes")
 #' sp_plot(NE_Lakes, formula = ~ELEV_CAT)
 #' sample <- grts(NE_Lakes, 30)
 #' sp_plot(sample, NE_Lakes)
 #' data("NLA_PNW")
 #' sp_plot(NLA_PNW, formula = ~BMMI)
+#' }
 sp_plot <- function(object, ...) {
   UseMethod("sp_plot", object)
 }
@@ -104,6 +106,12 @@ sp_plot.default <- function(object, formula = ~1, xcoord, ycoord, crs,
                             var_args = NULL, varlevel_args = NULL,
                             geom = FALSE, onlyshow = NULL, fix_bbox = TRUE, ...) {
 
+  # find system info
+  on_solaris <- Sys.info()[["sysname"]] == "SunOS"
+  if (on_solaris) {
+    stop("sp_plot() is not supported on Solaris.")
+  }
+
   # coerce to sf
   if (!inherits(object, "sf")) {
     object <- st_as_sf(object, coords = c(xcoord, ycoord), crs = crs)
@@ -290,6 +298,13 @@ sp_plot.default <- function(object, formula = ~1, xcoord, ycoord, crs,
 sp_plot.spdesign <- function(object, sframe = NULL, formula = ~siteuse, siteuse = NULL,
                              var_args = NULL, varlevel_args = NULL, geom = FALSE, onlyshow = NULL,
                              fix_bbox = TRUE, ...) {
+
+  # find system info
+  on_solaris <- Sys.info()[["sysname"]] == "SunOS"
+  if (on_solaris) {
+    stop("sp_plot() is not supported on Solaris.")
+  }
+
   if ((is.null(siteuse) & (!is.null(object$sites_near))) | "Near" %in% siteuse) {
     object$sites_near$siteuse <- "Near"
   }

diff --git a/R/sp_rbind.R b/R/sp_rbind.R
@@ -22,9 +22,9 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' sample <- grts(NE_Lakes, 50, n_over = 10)
 #' sample <- sp_rbind(sample)
-#' \dontrun{
 #' write_sf(sample, "mypath/sample.shp")
 #' }
 sp_rbind <- function(object, siteuse = NULL) {

diff --git a/R/sp_summary.R b/R/sp_summary.R
@@ -59,11 +59,13 @@
 #' @export
 #'
 #' @examples
+#' \dontrun{
 #' data("NE_Lakes")
 #' sp_summary(NE_Lakes, ELEV ~ 1)
 #' sp_summary(NE_Lakes, ~ ELEV_CAT * AREA_CAT)
 #' sample <- grts(NE_Lakes, 100)
 #' sp_summary(sample, ~ ELEV_CAT * AREA_CAT)
+#' }
 sp_summary <- function(object, ...) {
   UseMethod("sp_summary", object)
 }
@@ -72,6 +74,13 @@ sp_summary <- function(object, ...) {
 #' @method sp_summary default
 #' @export
 sp_summary.default <- function(object, formula = ~1, onlyshow = NULL, ...) {
+
+  # find system info
+  on_solaris <- Sys.info()[["sysname"]] == "SunOS"
+  if (on_solaris) {
+    stop("sp_summary() is not supported on Solaris.")
+  }
+
   # making formlist (utils.R)
   formlist <- make_formlist(formula, onlyshow, object)
   # making varsf (utils.R)

diff --git a/README.md b/README.md
@@ -78,15 +78,15 @@ citation(package = "spsurvey")
 #> To cite the spsurvey package in publications use:
 #> 
 #>   Dumelle, Michael., Kincaid, T. M., Olsen, A. R., and Weber, M. H. (2021). spsurvey:
-#>   Spatial Sampling Design and Analysis. R package version 5.0.0.
+#>   Spatial Sampling Design and Analysis. R package version 5.0.1.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
 #>   @Manual{,
 #>     title = {spsurvey: Spatial Sampling Design and Analysis},
 #>     author = {Michael Dumelle and Thomas M. Kincaid and Anthony R. Olsen and Marc H. Weber},
 #>     year = {2021},
-#>     note = {R package version 5.0.0},
+#>     note = {R package version 5.0.1},
 #>   }
 ```
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,51 +1,43 @@
-This is a major update introducing several updates to pre-existing functions
-Some of these changes are breaking; we alert users to this fact in the `NEWS.md` file
-and in a startup message upon loading the package. In addition, some 
-new functions were added.
+This is a minor update addressing Solaris performance problems.
 
 -------
 
 ## Test environments
-* Tests run on October 15, 2021 (rhub version 1.1.1)
+
+* Tests run on October 18, 2021 (rhub version 1.1.1)
 
 * Build reports can be viewed through their hyperlinked Build ID URLs
 
 * `rhub::check_for_cran()`
     * Platform: Windows Server 2008 R2 SP1, R-devel, 32/64 bit
         * Status: success (NOTE related to manual PDF size -- see next section)
-        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.0.tar.gz-2835f96162ea4b4fa9f946614b80775c
+        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.1.tar.gz-a4d656b6638b424ebe6d856cbafe69b5
     * Platform: Fedora Linux, R-devel, clang, gfortran
         * Status: success (NOTE related to manual PDF size -- see next section)
-        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.0.tar.gz-3e7a8d16eba44f46befc13a83b2680a6
+        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.1.tar.gz-5605a60bc9a244c9a98ec169dc2a6fc5
     * Platform: Ubuntu Linux 20.04.1 LTS, R-release, GCC
         * Status: SUCCESS (NOTE related to manual PDF size see next section)
-        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.0.tar.gz-cbb896af25454f17a7eaf4aac0d72d76
+        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.1.tar.gz-a3841f544902438cb731c8399e582bc5
 
 * `rhub::check_on_windows()`
     * Platform: Windows Server 2008 R2 SP1, R-release, 32/64 bit
         * success (NOTE related to manual PDF size -- see next section)
-        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.0.tar.gz-2c912c5200234b0e9f2d296457564757
+        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.1.tar.gz-54655dd37aa64eec800ba369ce921ecf
 
 * `rhub::check_on_linux()`
     * Platform: Debian Linux, R-release, GCC
         * success (NOTE related to manual PDF size -- see next section)
-        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.0.tar.gz-ee578c071fb14bf982b487bfa4c07b89
+        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.1.tar.gz-cf184d638b814ac3a2770048fdbc2645
 
-* `rhub::check_on_ubuntu()`
-    * Platform: Ubuntu Linux 20.04.1 LTS, R-release, GCC
-        * success (NOTE related to manual PDF size -- see next section)
-        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.0.tar.gz-921468a2297d4721a23c49fddae151d0
+* `rhub::check_on_solaris()`
+    * Platform: Oracle Solaris 10, x86, 32 bit, R-release
+        * success (NOTE related to panual PDF size -- see next section)
+        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.1.tar.gz-4b382f8214e24e3ab589d463fc93c417 
 
 * `rhub::check(platform = "macos-highsierra-release-cran")`
     * Platform: macOS 10.13.6 High Sierra, R-release, CRAN's setup
         * Status: SUCCESS (NOTE related to manual PDF size see next section)
-        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.0.tar.gz-1bba837e167b4ae5b111ad5ac445a936
-
-* GitHub actions (`usethis::use_github_action_check_standard()` also available [here](https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml))
-    * Platform: windows-latest (release), macOS-latest (release), ubuntu-20.04 (release), ubundo-20.04 (devel)
-    * Build ID: GitHub actions R-CMD-check results for spsurvey are available [here](https://github.com/USEPA/spsurvey/actions/workflows/R-CMD-check.yaml). This push corresponds to 
-    R-CMD-check 22 (news and cran comment updates) on October 15, 2021.
-
+        * Build ID: https://builder.r-hub.io/status/spsurvey_5.0.1.tar.gz-f1f08046f1894225a104b6020907d7b1
 
 ## R CMD check results
 
@@ -64,5 +56,4 @@ reflect the size of the final PDF manual installed upon package build.
 
 ## Downstream dependencies
 
-I have let the authors of packages that import and suggest spsurvey know that we 
-are releasing a major update.
+This minor update should not affect any downstream dependencies (apart from those impacted by the release of version 5.0.0)
diff --git a/inst/CITATION b/inst/CITATION
@@ -5,8 +5,8 @@ citEntry(
    title="spsurvey: Spatial Sampling Design and Analysis",
    author="Michael Dumelle, Thomas M. Kincaid, Anthony R. Olsen, and Marc H. Weber",
    year=2021,
-   note="R package version 5.0.0",
+   note="R package version 5.0.1",
    textVersion=paste("Dumelle, Michael., Kincaid, T. M., Olsen, A. R., and Weber, M. H. (2021).",
                      "spsurvey: Spatial Sampling Design and Analysis.",
-                     "R package version 5.0.0.")
+                     "R package version 5.0.1.")
 )
diff --git a/man/grts.Rd b/man/grts.Rd
diff --git a/man/irs.Rd b/man/irs.Rd
diff --git a/man/sp_balance.Rd b/man/sp_balance.Rd
diff --git a/man/sp_plot.Rd b/man/sp_plot.Rd
diff --git a/man/sp_rbind.Rd b/man/sp_rbind.Rd
diff --git a/man/sp_summary.Rd b/man/sp_summary.Rd