getting ready for CRAN

R/gscramble2newhybrids.R

@@ -20,7 +20,9 @@
 #' @param s a single regular expressions that matches individuals that
 #' should be given the -s option. For example "SH|CCT"
 #' @param retain a vector of loci to retain.
-#' @param outfile path to the file to write the newhybrids data set to.
+#' @param outfile path to the file to write the newhybrids data set to. For CRAN
+#' compliance, this is, by default, a temp file. But you can change it to be
+#' anything valid.
 #' @details This function relies a lot on some tidyverse functions
 #' for pivoting, etc.  As such, it is not intended for data sets with
 #' tens of thousands of markers.  You oughtn't be using NewHybrids with
@@ -31,14 +33,20 @@
 #'   - `allele_names`: Allele names.
 #' @export
 #' @examples
+#' # get output from segments2markers():
+#' example("segments2markers")
+#' # copy that result to a new variable
+#' M <- s2m_result
+#'
+#' # then run it
 #' gscramble2newhybrids(M, M_meta)
 gscramble2newhybrids <- function(
     M,
     M_meta,
     z = NULL,
     s = NULL,
     retain = NULL,
-    outfile = "gscram-newhybs.txt"
+    outfile = tempfile()
   ) {
   headers <- paste(rep(M_meta$variant_id, each = 2), "____", c(1,2), sep = "")
 

cran-comments.md

@@ -1,11 +1,25 @@
 ## R CMD check results
 
-## Test environments
+* Local
+  - macOS 12.7.2, using R 4.3.1
+    + 0 errors | 0 warnings | 0 notes
 
 * Using GitHub Actions
   - macOS 12.7.1 21G920, R 4.3.2
+    + 0 errors | 0 warnings | 0 notes
+  - ubuntu latest (22.04.3), devel, using R Under development (unstable) (2024-02-05 r85863)
+    + 0 errors | 0 warnings | 0 notes
+  - ubuntu latest (22.04.3), release, using R  4.3.2 (2023-10-31)
+    + 0 errors | 0 warnings | 0 notes
+  - ubuntu latest (22.04.3), old-rel1, using R 4.2.3 (2023-03-15)
+    + 0 errors | 0 warnings | 0 notes
+  - windows latest (Microsoft Windows Server 2022 10.0.20348)  using R 4.3.2 (2023-10-31 ucrt)
+    + 0 errors | 0 warnings | 0 notes
 
-## R CMD check results
+
+* check_win()
+  - release
+  - devel
 
 MAC, local: 0 errors | 0 warnings | 1 notes
   - 1 note =  GNU make is a SystemRequirements (this is for RcppParallel)
@@ -42,8 +56,3 @@ Currently no known reverse dependencies
 
 ## User Notices
 
-* This release fixes a few NOTES that Kurt Hornik emailed me about.
-
-0 errors | 0 warnings | 1 note
-
-* This is a new release.