Delete temp files

RcppTskit/R/Class-TableCollection.R

@@ -65,6 +65,7 @@ TableCollection <- R6Class(
     #' dump_file <- tempfile()
     #' tc$dump(dump_file)
     #' tc$write(dump_file) # alias
+    #' \dontshow{file.remove(dump_file)}
     dump = function(file) {
       tc_ptr_dump(self$pointer, file = file, options = 0L)
     },

RcppTskit/R/Class-TreeSequence.R

@@ -71,6 +71,7 @@ TreeSequence <- R6Class(
     #' dump_file <- tempfile()
     #' ts$dump(dump_file)
     #' ts$write(dump_file) # alias
+    #' \dontshow{file.remove(dump_file)}
     dump = function(file) {
       ts_ptr_dump(self$pointer, file = file, options = 0L)
     },

RcppTskit/src/RcppTskit.cpp

@@ -225,6 +225,7 @@ SEXP tc_ptr_load(const std::string file, const int options = 0) {
 // ts_ptr <- RcppTskit:::ts_ptr_load(ts_file)
 // dump_file <- tempfile()
 // RcppTskit:::ts_ptr_dump(ts_ptr, dump_file)
+// file.remove(dump_file)
 // [[Rcpp::export]]
 void ts_ptr_dump(const SEXP ts, const std::string file, const int options = 0) {
   const tsk_flags_t dump_options =
@@ -250,6 +251,7 @@ void ts_ptr_dump(const SEXP ts, const std::string file, const int options = 0) {
 // tc_ptr <- RcppTskit:::tc_ptr_load(ts_file)
 // dump_file <- tempfile()
 // RcppTskit:::tc_ptr_dump(tc_ptr, dump_file)
+// file.remove(dump_file)
 // [[Rcpp::export]]
 void tc_ptr_dump(const SEXP tc, const std::string file, const int options = 0) {
   const tsk_flags_t dump_options =

RcppTskit/tests/testthat/test_load_summary_and_dump.R

@@ -390,6 +390,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   ts_ptr_dump(ts_ptr, dump_file)
   rm(ts_ptr)
   ts_ptr <- ts_ptr_load(dump_file)
+  file.remove(dump_file)
 
   # Simple comparison of summaries
   n <- ts_ptr_summary(ts_ptr)
@@ -438,6 +439,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   rm(tc_ptr)
   tc_ptr <- tc_ptr_load(dump_file)
   ts_ptr <- ts_ptr_load(dump_file)
+  file.remove(dump_file)
 
   # Simple comparison of summaries
   n_ts <- ts_ptr_summary(ts_ptr)
@@ -474,6 +476,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   ts$dump(dump_file)
   rm(ts)
   ts <- ts_load(dump_file)
+  file.remove(dump_file)
 
   # Simple comparison of summaries
   n_ptr <- ts_ptr_summary(ts$pointer)
@@ -515,6 +518,7 @@ test_that("ts/tc_load(), ts/tc_summary*(), and ts/tc_dump(x) work", {
   tc$dump(dump_file)
   rm(tc)
   tc <- tc_load(dump_file)
+  file.remove(dump_file)
 
   # Simple comparison of summaries
   n_ptr <- tc_ptr_summary(tc$pointer)

RcppTskit/vignettes/RcppTskit_intro.qmd

@@ -276,6 +276,7 @@ ts$dump(file = ts_file)
 # ... and to bring it back to R, use ...
 ts2 <- ts_load(ts_file)
 ts$num_individuals() # 2 (if you have run the above Python code)
+file.remove(ts_file)
 
 # You can work similarly with table collection between R & Python
 tc <- ts$dump_tables()