File move uses fs when installed, instead of file.rename, which r…

…equires the source and destination to be on the same disk

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: raveio
 Type: Package
 Title: File-System Toolbox for RAVE Project
-Version: 0.9.0.66
+Version: 0.9.0.67
 Language: en-US
 Authors@R: c(
     person("Zhengjia", "Wang", email = "[email protected]", role = c("aut", "cre", "cph")),

R/cmd-aaa.R

@@ -60,7 +60,7 @@ cmd_execute <- function(script, script_path, command = "bash", dry_run = FALSE,
       if(file.exists(to_path)) {
         unlink(backup_path)
       } else {
-        file.rename(backup_path, to_path)
+        file_move(backup_path, to_path)
       }
     }
   }

R/csv.R

@@ -27,7 +27,7 @@ safe_write_csv <- function(x, file, ..., quiet = FALSE){
     if(!quiet){
       catgl('Renaming file {file}\n  >> {oldfile}')
     }
-    file.rename(file, oldfile)
+    file_move(file, oldfile)
   }
   args <- list(...)
   rn <- args$row.names

R/csv2.R

@@ -170,7 +170,7 @@ export_table <- function(x, file, format = c("auto", "csv", "csv.zip", "h5", "fs
       })
       data.table::fwrite(x = x, file = tf, ...)
       utils::zip(zipfile = zf, files = tf, extras='-j')
-      file.rename(zf, file)
+      file_move(zf, file)
     },
     "fst" = {
       fst::write_fst(x = x, path = file, compress = 99)
@@ -211,7 +211,7 @@ export_table <- function(x, file, format = c("auto", "csv", "csv.zip", "h5", "fs
       # save meta information
       save_h5(x = jsonlite::serializeJSON(meta), file = h5file, name = "__meta__", replace = TRUE, ctype = "character", quiet = TRUE)
 
-      file.rename(h5file, file)
+      file_move(h5file, file)
     },
     "rds" = {
       saveRDS(object = x, file = file, ...)

R/pipeline-serializer.R

@@ -408,7 +408,7 @@ tfmtreg_filearray <- function() {
                     copy.date = TRUE, recursive = TRUE,
                     overwrite = TRUE)
           orig_name <- basename(filebase_orig)
-          file.rename(
+          file_move(
             file.path(filebase_dir, orig_name),
             filebase
           )

R/units.R

@@ -289,7 +289,7 @@ backup_file <- function(path, remove = FALSE, quiet = FALSE) {
   path2 <- file.path(dname, bname2)
 
   if( remove ) {
-    file.rename(from = path, to = path2)
+    file_move(from = path, to = path2)
   } else {
     if(is_dir) {
       dir_create2(path2)

R/utils-archive.R

@@ -386,7 +386,7 @@ archive_subject <- function(
     if(file.exists(path)) {
       backup_file(path, remove = TRUE)
     }
-    file.rename(zipfile_name, path)
+    file_move(zipfile_name, path)
   } else {
     path <- zipfile_name
   }
@@ -545,7 +545,7 @@ install_subject <- function(
 
       if( backup ) {
         new_path <- backup_file(subject$preprocess_settings$raw_path, remove = TRUE)
-        file.rename(subject$path, file.path(dirname(subject$path), filenames(new_path)))
+        file_move(subject$path, file.path(dirname(subject$path), filenames(new_path)))
       }
     }
   }

R/zzz.R

@@ -33,6 +33,19 @@ normalize_path <- function(path, must_work = NA) {
   gsub("[/|\\\\]+", "/", path)
 }
 
+file_move <- function(from, to) {
+  if(dipsaus::package_installed("fs")) {
+    fs <- asNamespace("fs")
+    impl <- fs$file_move
+    if(is.function(impl)) {
+      impl(path = from, new_path = to)
+      return(invisible(to))
+    }
+  }
+  file.rename(from = from, to = to)
+  return(invisible(to))
+}
+
 safe_system <- function(cmd, ..., intern = TRUE, ignore.stderr = TRUE,
                         minimized = TRUE, invisible = TRUE, show.output.on.console = TRUE){
   suppressWarnings({