From 1b624bd56bd8b2a4672238a77c750da2f7145213 Mon Sep 17 00:00:00 2001
From: "Daniel R. Roe" <daniel.r.roe@gmail.com>
Date: Fri, 18 Mar 2022 15:10:23 -0400
Subject: [PATCH] Fix memory error when running interactive mode with long
 command line (#959)

* Protect against memory overflow when running interactive mode with a long command line

* 6.4.4. Revision bump for memory overflow with interactive mode + long command line fix.

* Fix printf format

* Protect against potential buffer overruns
---
 src/Action_Keep.cpp         | 2 +-
 src/Cpptraj.cpp             | 7 +++++--
 src/Version.h               | 2 +-
 src/vmdplugin/dtrplugin.cpp | 6 +++---
 4 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/Action_Keep.cpp b/src/Action_Keep.cpp
index f73fe62ae5..a70016acbf 100644
--- a/src/Action_Keep.cpp
+++ b/src/Action_Keep.cpp
@@ -164,7 +164,7 @@ Action::RetType Action_Keep::Setup(ActionSetup& setup)
       if (resSize == -1)
         resSize = setup.Top().Res(*rnum).NumAtoms();
       else if (setup.Top().Res(*rnum).NumAtoms() != resSize) {
-        mprinterr("Error: Residue '%s' size (%i) != first residue size (%s)\n",
+        mprinterr("Error: Residue '%s' size (%i) != first residue size (%i)\n",
                   setup.Top().TruncResNameNum(*rnum).c_str(),
                   setup.Top().Res(*rnum).NumAtoms(), resSize);
         return Action::ERR;
diff --git a/src/Cpptraj.cpp b/src/Cpptraj.cpp
index f6857fab2f..5d94b8dacb 100644
--- a/src/Cpptraj.cpp
+++ b/src/Cpptraj.cpp
@@ -650,8 +650,11 @@ int Cpptraj::Interactive() {
   if (logfile_.IsOpen()) {
     // Write logfile header entry: date, cmd line opts, topologies
     logfile_.Printf("# %s\n", TimeString().c_str());
-    if (!commandLine_.empty())
-      logfile_.Printf("# Args: %s\n", commandLine_.c_str());
+    if (!commandLine_.empty()) {
+      logfile_.Printf("# Args: ");
+      logfile_.Write(commandLine_.c_str(), commandLine_.size());
+      logfile_.Printf("\n");
+    }
     DataSetList tops = State_.DSL().GetSetsOfType("*", DataSet::TOPOLOGY);
     if (!tops.empty()) {
       logfile_.Printf("# Loaded topologies:\n");
diff --git a/src/Version.h b/src/Version.h
index 85d8f565bd..2c003ddddc 100644
--- a/src/Version.h
+++ b/src/Version.h
@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V6.4.3"
+#define CPPTRAJ_INTERNAL_VERSION "V6.4.4"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif
diff --git a/src/vmdplugin/dtrplugin.cpp b/src/vmdplugin/dtrplugin.cpp
index cdaa7ff3ea..3f92f8de20 100644
--- a/src/vmdplugin/dtrplugin.cpp
+++ b/src/vmdplugin/dtrplugin.cpp
@@ -652,7 +652,7 @@ static inline std::string addslash(const std::string& s){
     return (s.rbegin()[0] == '/') ? s : s + "/";
 }
 
-#define DD_RELPATH_MAXLEN (9) 
+#define DD_RELPATH_MAXLEN (32) 
 static std::string 
 DDreldir(const std::string& fname, int ndir1, int ndir2){
 
@@ -712,7 +712,7 @@ void DDmkdir(const std::string &dirpath, mode_t mode, int ndir1, int ndir2){
 	throw DDException("fclose(.ddparams)", errno);
 
     for(int i=0; i<ndir1; ++i){
-	char sub[6];
+	char sub[16];
 	sprintf(sub, "%03x/", i);
 	std::string dirsub = dpslash + sub;
         {
@@ -720,7 +720,7 @@ void DDmkdir(const std::string &dirpath, mode_t mode, int ndir1, int ndir2){
 		throw DDException("mkdir " + dirsub, errno);
 	}
 	for(int j=0; j<ndir2; ++j){
-	    char subsub[6];
+	    char subsub[16];
 	    sprintf(subsub, "%03x", j);
 	    std::string dirsubsub = dirsub + subsub;
 	    if( mkdir(dirsubsub.c_str(), mode) < 0 ) // NOT openmode!