From f2379acaf4cfdfe49d561a63726629e5ecf05153 Mon Sep 17 00:00:00 2001
From: redae <elhore.reda@gmail.com>
Date: Sun, 1 Sep 2019 13:15:17 +0100
Subject: [PATCH 1/4] Using forward slash to build a full path consistently
 with the output of file.expand function

---
 R/misc-functions.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/misc-functions.R b/R/misc-functions.R
index 2054214..3373d93 100644
--- a/R/misc-functions.R
+++ b/R/misc-functions.R
@@ -9,7 +9,7 @@
   
   # Parse file name and path
   if (file == "") file <- paste0("ukb-schemas-", date_str, ".sqlite")
-  full_path <- paste0(path.expand(path), "\\", file)
+  full_path <- paste0(path.expand(path), "/", file)
   
   # If `file`` exists, session is `interactive()` and `!overwrite`, then prompt 
   # to overwrite the file
@@ -92,4 +92,4 @@
   
   invisible(TRUE)
   
-}
\ No newline at end of file
+}

From 679260c1f8c50ae251ccb883effe62589ddb0bec Mon Sep 17 00:00:00 2001
From: redae <elhore.reda@gmail.com>
Date: Sun, 1 Sep 2019 13:16:55 +0100
Subject: [PATCH 2/4] Added a manual check for open connections in Unix systems
 before trying to delete the database file

---
 R/misc-functions.R | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/R/misc-functions.R b/R/misc-functions.R
index 3373d93..f519599 100644
--- a/R/misc-functions.R
+++ b/R/misc-functions.R
@@ -22,8 +22,18 @@
     }
     if (!isTRUE(overwrite)) 
       stop(UKBSCHEMAS_ERRORS$OVERWRITE)
-    else tryCatch(
-      file.remove(full_path),
+    else tryCatch({
+      if (.Platform$OS.type == "unix"){
+          sys_command <- paste("lsof", full_path, "| wc -l")
+          processes_using_file <- as.numeric(system(sys_command, intern = TRUE,
+                                                    ignore.stdout = TRUE,
+                                                    ignore.stderr = TRUE))
+          if (processes_using_file>1) {
+            stop(UKBSCHEMAS_ERRORS$FAILED_OVERWRITE)
+          }
+        }
+        file.remove(full_path)
+      },
       error = function(err) {
         stop(UKBSCHEMAS_ERRORS$FAILED_OVERWRITE)
       },
@@ -92,4 +102,4 @@
   
   invisible(TRUE)
   
-}
+}
\ No newline at end of file

From 20bbc94b9609757ec74ad19dc5b0e2af6f1f2059 Mon Sep 17 00:00:00 2001
From: redae <elhore.reda@gmail.com>
Date: Sun, 1 Sep 2019 13:42:45 +0100
Subject: [PATCH 3/4] Updated test files. Not to skip when system is not
 windows

---
 tests/testthat/test-save-db.R       | 3 ---
 tests/testthat/test-ukbschemas-db.R | 3 ---
 2 files changed, 6 deletions(-)

diff --git a/tests/testthat/test-save-db.R b/tests/testthat/test-save-db.R
index 81c94a9..85ac88c 100644
--- a/tests/testthat/test-save-db.R
+++ b/tests/testthat/test-save-db.R
@@ -72,9 +72,6 @@ test_that("save_db() fails on overwrite = FALSE, non-interactive", {
 
 test_that("save_db() fails to overwrite when db is connected", {
   
-  # This only seems to work on Windows
-  skip_if_not(.Platform$OS.type == "windows", "Skipping test if not Windows")
-  
   db_file <- test_db_file()
   
   expect_error(
diff --git a/tests/testthat/test-ukbschemas-db.R b/tests/testthat/test-ukbschemas-db.R
index 75033cc..70de563 100644
--- a/tests/testthat/test-ukbschemas-db.R
+++ b/tests/testthat/test-ukbschemas-db.R
@@ -84,9 +84,6 @@ test_that("ukbschemas_db() fails on overwrite = FALSE, non-interactive", {
 
 test_that("ukbschemas_db() fails to overwrite when db is connected", {
   
-  # This only seems to work on Windows
-  skip_if_not(.Platform$OS.type == "windows", "Skipping test if not Windows")
-  
   db_file <- test_db_file()
   
   expect_error(

From d9571bdcde2dfb2adb6cb5dd47cc8b312819286f Mon Sep 17 00:00:00 2001
From: redae <elhore.reda@gmail.com>
Date: Sun, 1 Sep 2019 15:22:27 +0100
Subject: [PATCH 4/4] Prefixed row_number() with dplyr::. Not doing so is
 deprecated, and the warning indicating that was making the build fail.

---
 R/tidy-schemas.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/tidy-schemas.R b/R/tidy-schemas.R
index 1d34bcf..1397e5e 100644
--- a/R/tidy-schemas.R
+++ b/R/tidy-schemas.R
@@ -61,7 +61,7 @@
         dplyr::mutate(.x, parent_id = NA, selectable = NA) %>%
           dplyr::mutate(type = type, value = as.character(value)) %>%
           dplyr::group_by(encoding_id) %>%
-          dplyr::mutate(code_id = row_number()) %>%
+          dplyr::mutate(code_id = dplyr::row_number()) %>%
           dplyr::ungroup()
       }
     )