Prepare for CRAN v0.1.10 release

* Updated dependencies `spatstat.core` and `spatstat.linnet` packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in `spatstat.core` were moved to a new package `spatstat.random` * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends * `spatstat.geom` is now Imports * `dplyr`, `ncdfFlow`, `flowWorkspaceData`, and `usethis` now Suggests (for generating random data set `randCyto`) * Fixed annotation typos in the vignette. Removed packages no longer used in the vignette
lance-waller-lab · Feb 4, 2022 · a7010be · a7010be
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gateR
 Type: Package
 Title: Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation
-Version: 0.1.9
-Date: 2021-06-20
+Version: 0.1.10
+Date: 2022-02-04
 Authors@R: 
     c(person(given = "Ian D.",
              family = "Buller",
@@ -41,13 +41,9 @@ License: Apache License (>= 2.0)
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Depends: 
-    R (>= 3.5.0),
-    spatstat.geom,
-    spatstat.core,
-    spatstat.linnet,
-    spatstat (>= 2.0-0)
+    R (>= 3.5.0)
 Imports: 
     fields,
     graphics,
@@ -57,13 +53,19 @@ Imports:
     rlang,
     sparr,
     SpatialPack,
+    spatstat.geom,
     stats,
     tibble,
+    tools,
     utils
 Suggests:
+    dplyr,
+    flowWorkspaceData,
+    ncdfFlow,
     R.rsp,
     spelling,
-    testthat
+    testthat,
+    usethis
 VignetteBuilder: R.rsp
 Language: en-US
 URL: https://github.com/Waller-SUSAN/gateR

diff --git a/NAMESPACE b/NAMESPACE
@@ -6,10 +6,6 @@ export(lrr_plot)
 export(pval_correct)
 export(pval_plot)
 export(rrs)
-import(spatstat)
-import(spatstat.core)
-import(spatstat.geom)
-import(spatstat.linnet)
 importFrom(SpatialPack,modified.ttest)
 importFrom(fields,image.plot)
 importFrom(grDevices,chull)

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,16 @@
 # gateR (development version)
 
+# gateR v0.1.10
+* Updated dependencies `spatstat.core` and `spatstat.linnet` packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in `spatstat.core` were moved to a new package `spatstat.random`
+  * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends
+  * `spatstat.geom` is now Imports
+* `dplyr`, `ncdfFlow`, `flowWorkspaceData`, and `usethis` now Suggests (for generating random data set `randCyto`)
+* Fixed annotation typos in the vignette. Removed packages no longer used in the vignette 
+
 # gateR v0.1.9
 * Now `rlang` is in Depends. 
-* Output for `gating()` now includes a diagnostic message saved as a character string for reference in a slot called `note`.
-* A diagnostic message can be viewed running `rlang::last_error()$out$note` after the unsuccessful run of `gating()`.
+* Output for `gating()` now includes a diagnostic message saved as a character string for reference in a slot called `note`
+* A diagnostic message can be viewed running `rlang::last_error()$out$note` after the unsuccessful run of `gating()`
 * Removed redundant `@importFrom fields image.plot` in 'package.R'
 
 # gateR v0.1.8

diff --git a/R/package.R b/R/package.R
@@ -41,10 +41,7 @@ NULL
 #' @importFrom rlang abort inform
 #' @importFrom sparr OS risk
 #' @importFrom SpatialPack modified.ttest
+#' @importFrom spatstat.geom as.im cut.im marks owin ppp
 #' @importFrom stats na.omit pnorm relevel
 #' @importFrom tibble add_column
-#' @import spatstat.geom
-#' @import spatstat.core
-#' @import spatstat.linnet
-#' @import spatstat
 NULL
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,21 +1,24 @@
-## This is the nineth resubmission
+## This is the tenth resubmission
 
 * Updates since previous submission:
-  * Now `rlang` is in Depends. 
-  * Output for `gating()` now includes a diagnostic message saved as a character string for reference in a slot called `note`.
-  * A diagnostic message can be viewed running `rlang::last_error()$out$note` after the unsuccessful run of `gating()`.
-  * Removed redundant `@importFrom fields image.plot` in 'package.R'
-
+  * Updated dependencies `spatstat.core` and `spatstat.linnet` packages based on feedback from the Spatstat Team (Adrian Baddeley and Ege Rubak). All random generators in `spatstat.core` were moved to a new package `spatstat.random`
+    * `spatstat.geom`, `spatstat.core`, `spatstat.linnet`, and `spatstat (>=2.0-0)` are no longer Depends
+    * `spatstat.geom` is now Imports
+  * Fixed annotation typos in the vignette. Removed packages no longer used in the vignette 
+  * `dplyr`, `ncdfFlow`, `flowWorkspaceData`, and `usethis` now Suggests (for generating random data set `randCyto`)
+
 * Documentation for `pval_correct()` references doi <https://doi.org/10.2307/2283989> and <https://doi.org/10.1214/aop/1176996176> that throw NOTES in win-builder, Fedora Linux, and Ubuntu Linux but these are valid URLs
 
 ## Test environments
-* local OS X install, R 4.0.4
+* local OS X install, R 4.1.2
 * win-builder, (devel, release, oldrelease)
 * Rhub
   * Fedora Linux, R-devel, clang, gfortran
-  * Ubuntu Linux 16.04 LTS, R-release, GCC
-  * Windows Server 2008 R2 SP1, R-devel, 32/64 bit
+  * Ubuntu Linux 20.04.1 LTS, R-release, GCC
+  * Windows Server 2022, R-devel, 64 bit
+  * Windows Server 2008 R2 SP1, R-release, 32⁄64 bit
   * Oracle Solaris 10, x86, 32 bit, R-release
+  * macOS 10.13.6 High Sierra, R-release, CRAN's setup
 
 ## R CMD check results
 0 errors | 0 warnings | 0 notes

diff --git a/tests/testthat/test-lotrrs.R b/tests/testthat/test-lotrrs.R
@@ -9,7 +9,6 @@ fubar <- fubar1 <- randCyto
 fubar$g1 <- as.numeric(fubar$g1)
 fubar1$g2 <- as.numeric(fubar1$g2)
 
-
 # Tests
 
 test_that("lotrrs throws error with invalid arguments", {

diff --git a/vignettes/vignette.Rmd b/vignettes/vignette.Rmd
@@ -36,12 +36,12 @@ This vignette provides an implementation of the gateR package using a randomly g
 We start with the necessary packages and seed for the vignette.
 
 ```{r packages}
-  loadedPackages <- c("gateR", "graphics", "maptools", "raster", "sp", "sparr", "spatstat", "stats", "tibble", "utils")
+  loadedPackages <- c("gateR", "graphics", "stats", "tibble", "utils")
   invisible(lapply(loadedPackages, library, character.only = TRUE))
   set.seed(1234) # for reproducibility
 ```
 
-### Generate random toy data using the `spatstat` package
+### Generate random toy data
 
 Unique function to randomly generate data multivariate normal (MVN) around a central point. Parameters include the centroid coordinates (`centre`), number of observations to generate (`ncell`), and the standard deviation of the normal distribution (`scalar`). 
 

diff --git a/vignettes/vignette.html b/vignettes/vignette.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,7 +9,6 @@ fubar <- fubar1 <- randCyto @@
     fubar$g1 <- as.numeric(fubar$g1)
     fubar1$g2 <- as.numeric(fubar1$g2)
     # Tests
     test_that("lotrrs throws error with invalid arguments", {
@@ Expand Down @@