From 65c0982cdaa2a31bb3ccc61463e18d8b9f9c066a Mon Sep 17 00:00:00 2001
From: Michael Chirico <chiricom@google.com>
Date: Wed, 19 Jun 2024 08:00:33 -0700
Subject: [PATCH 1/5] Directly include system headers

Found by `clang-tidy`:

https://clang.llvm.org/extra/clang-tidy/checks/misc/include-cleaner.html

 - cctype --> toupper()
 - cstddef --> size_t

There are several other findings related to `libuv` that I'm omitting here e.g.

> no header providing "uv_fs_req_cleanup" is directly included

As well as ones that are really not standard for R packages:

> no header providing "NULL" is directly included

Happy to provide the full output if requested; sticking to a more minimal version of standard system headers here for now.
---
 src/utils.cc | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/utils.cc b/src/utils.cc
index 84824313..731e6190 100644
--- a/src/utils.cc
+++ b/src/utils.cc
@@ -1,3 +1,5 @@
+#include <cctype>
+#include <cstddef>
 #include <string>
 
 #include "utils.h"

From fbfe61f042b482e1772a48698ddb7463562ee930 Mon Sep 17 00:00:00 2001
From: Michael Chirico <michaelchirico4@gmail.com>
Date: Wed, 19 Jun 2024 08:01:47 -0700
Subject: [PATCH 2/5] string --> std::string

---
 src/path.cc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/path.cc b/src/path.cc
index 354a75dc..63fa2ff2 100644
--- a/src/path.cc
+++ b/src/path.cc
@@ -2,6 +2,7 @@
 
 #include <cstdlib>
 #include <cstring>
+#include <string>
 
 #include "Rinternals.h"
 #include "error.h"

From 1c8f911713a8d0f1dfefae7332683b55eec143c1 Mon Sep 17 00:00:00 2001
From: Michael Chirico <michaelchirico4@gmail.com>
Date: Wed, 19 Jun 2024 08:02:22 -0700
Subject: [PATCH 3/5] another size_t

---
 src/id.cc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/id.cc b/src/id.cc
index cc4165cb..b07fe723 100644
--- a/src/id.cc
+++ b/src/id.cc
@@ -1,3 +1,4 @@
+#include <cstddef>
 #include <string>
 #include <vector>
 

From b419f62cd29bfd7ee1adc68e1c3f1563ec778e8e Mon Sep 17 00:00:00 2001
From: Michael Chirico <michaelchirico4@gmail.com>
Date: Wed, 19 Jun 2024 08:03:33 -0700
Subject: [PATCH 4/5] cstdio --> snprintf

---
 src/file.cc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/file.cc b/src/file.cc
index 20b898c9..202be46a 100644
--- a/src/file.cc
+++ b/src/file.cc
@@ -2,6 +2,7 @@
 #define __STDC_FORMAT_MACROS 1
 #endif
 
+#include <cstdio>
 #include <string>
 #include <vector>
 #include <inttypes.h>

From d0276d3413cb39338733239fb837202efe99db12 Mon Sep 17 00:00:00 2001
From: Michael Chirico <michaelchirico4@gmail.com>
Date: Wed, 19 Jun 2024 08:03:57 -0700
Subject: [PATCH 5/5] Another std::string

---
 src/dir.cc | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/dir.cc b/src/dir.cc
index 2d2c9807..d1f0bb89 100644
--- a/src/dir.cc
+++ b/src/dir.cc
@@ -1,5 +1,6 @@
 #include <cstring>
 #include <limits>
+#include <string>
 #include <sys/stat.h>
 
 #include "getmode.h"