Cleanup some warnings in Java JNI code (#2034) (#2099)

4 files changed, 146 insertions, 108 deletions

diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index eeed806..0bc17d1 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -1067,10 +1067,9 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
     H5T_class_t type_class;
     hsize_t     dims[H5S_MAX_RANK];
     hid_t       sid = H5I_INVALID_HID;
-    jsize       n;
+    jsize       n   = 0;
     htri_t      vl_data_class;
-    herr_t      status = FAIL;
-    jboolean    readBufIsCopy;
+    herr_t      status  = FAIL;
     jbyteArray *readBuf = NULL;
 
     UNUSED(clss);
@@ -1104,7 +1103,6 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
         jobject    *jList  = NULL;
 
         size_t i, j, x;
-        char  *cp_vp = NULL;
 
         if (!(typeSize = H5Tget_size(mem_type_id)))
             H5_LIBRARY_ERROR(ENVONLY);
@@ -1123,7 +1121,7 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
             H5_LIBRARY_ERROR(ENVONLY);
 
         /* Cache class types */
-        jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
+        /* jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
         jclass cByte   = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
         jclass cShort  = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
         jclass cInt    = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
@@ -1131,8 +1129,10 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
         jclass cFloat  = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
         jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
 
+        /*
         jmethodID boolValueMid =
             ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
+        */
         jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
         jmethodID shortValueMid =
             ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
@@ -1149,21 +1149,28 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
 
         /* Convert each element to a list */
         for (i = 0; i < (size_t)n; i++) {
+            hvl_t vl_elem;
+
             // The list we're going to return:
             if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
                 CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
-            cp_vp = (char *)rawBuf + i * typeSize;
             /* Get the number of sequence elements */
-            jsize nelmts = ((hvl_t *)cp_vp)->len;
+            HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
+
+            jsize nelmts = (jsize)vl_elem.len;
+            if (vl_elem.len != (size_t)nelmts)
+                H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadVL: overflow of number of VL elements");
+            if (nelmts < 0)
+                H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: number of VL elements < 0");
 
             jobject jobj = NULL;
-            for (j = 0; j < nelmts; j++) {
+            for (j = 0; j < (size_t)nelmts; j++) {
                 switch (vlClass) {
                     /* case H5T_BOOL: {
                         jboolean boolValue;
-                        for (x = 0; x < (int)vlSize; x++) {
-                            ((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x];
+                        for (x = 0; x < vlSize; x++) {
+                            ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
                         }
 
                         jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
@@ -1174,8 +1181,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
                         switch (vlSize) {
                             case sizeof(jbyte): {
                                 jbyte byteValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj =
@@ -1185,8 +1192,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
                             }
                             case sizeof(jshort): {
                                 jshort shortValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
@@ -1196,8 +1203,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
                             }
                             case sizeof(jint): {
                                 jint intValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
@@ -1206,8 +1213,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
                             }
                             case sizeof(jlong): {
                                 jlong longValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj =
@@ -1222,8 +1229,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
                         switch (vlSize) {
                             case sizeof(jfloat): {
                                 jfloat floatValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
@@ -1233,8 +1240,8 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
                             }
                             case sizeof(jdouble): {
                                 jdouble doubleValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
@@ -1248,14 +1255,19 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
                     case H5T_REFERENCE: {
                         jboolean bb;
                         jbyte   *barray = NULL;
-                        if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize)))
+
+                        jsize byteArraySize = (jsize)vlSize;
+                        if (vlSize != (size_t)byteArraySize)
+                            H5_JNI_FATAL_ERROR(ENVONLY, "H5AreadVL: overflow of byteArraySize");
+
+                        if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
                             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
                         PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
                                        "readVL reference: byte array not pinned");
 
-                        for (x = 0; x < (int)vlSize; x++) {
-                            barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                        for (x = 0; x < vlSize; x++) {
+                            barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x];
                         }
                         if (barray)
                             UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
@@ -1340,7 +1352,6 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
         jobject    *jList  = NULL;
 
         size_t i, j, x;
-        char  *cp_vp = NULL;
 
         if (!(typeSize = H5Tget_size(mem_type_id)))
             H5_LIBRARY_ERROR(ENVONLY);
@@ -1356,7 +1367,7 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
             H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate raw VL write buffer");
 
         /* Cache class types */
-        jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
+        /* jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
         jclass cByte   = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
         jclass cShort  = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
         jclass cInt    = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
@@ -1364,7 +1375,7 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
         jclass cFloat  = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
         jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
 
-        jmethodID boolValueMid   = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z");
+        /* jmethodID boolValueMid   = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */
         jmethodID byteValueMid   = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
         jmethodID shortValueMid  = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
         jmethodID intValueMid    = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
@@ -1374,6 +1385,8 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
 
         /* Convert each list to a vlen element */
         for (i = 0; i < (size_t)n; i++) {
+            hvl_t vl_elem;
+
             if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
                 CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
@@ -1387,22 +1400,25 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
             jobjectArray array   = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
             jsize        jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
 
-            cp_vp                 = (char *)rawBuf + i * typeSize;
-            ((hvl_t *)cp_vp)->len = jnelmts;
+            if (jnelmts < 0)
+                H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AwriteVL: number of VL elements < 0");
 
-            if (NULL == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize)))
+            HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
+            vl_elem.len = (size_t)jnelmts;
+
+            if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
                 H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5AwriteVL: failed to allocate vlen ptr buffer");
 
             jobject jobj = NULL;
-            for (j = 0; j < (int)jnelmts; j++) {
+            for (j = 0; j < (size_t)jnelmts; j++) {
                 if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
                     CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
                 switch (vlClass) {
                     /* case H5T_BOOL: {
                             jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
-                            for (x = 0; x < (int)vlSize; x++) {
-                                ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x];
+                            for (x = 0; x < vlSize; x++) {
+                                ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
                             }
                             break;
                     } */
@@ -1410,29 +1426,29 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
                         switch (vlSize) {
                             case sizeof(jbyte): {
                                 jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x];
                                 }
                                 break;
                             }
                             case sizeof(jshort): {
                                 jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x];
                                 }
                                 break;
                             }
                             case sizeof(jint): {
                                 jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x];
                                 }
                                 break;
                             }
                             case sizeof(jlong): {
                                 jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
                                 }
                                 break;
                             }
@@ -1443,15 +1459,15 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
                         switch (vlSize) {
                             case sizeof(jfloat): {
                                 jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x];
                                 }
                                 break;
                             }
                             case sizeof(jdouble): {
                                 jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
                                 }
                                 break;
                             }
@@ -1460,8 +1476,8 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
                     }
                     case H5T_REFERENCE: {
                         jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
-                        for (x = 0; x < (int)vlSize; x++) {
-                            ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x];
+                        for (x = 0; x < vlSize; x++) {
+                            ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
                         }
                         ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
                         break;
@@ -1472,6 +1488,9 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
                 }
                 ENVPTR->DeleteLocalRef(ENVONLY, jobj);
             }
+
+            HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t));
+
             ENVPTR->DeleteLocalRef(ENVONLY, jList);
         } /* end for (i = 0; i < n; i++) */
 
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index 4b32af3..c7d7c5d 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -1078,8 +1078,7 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
     H5T_class_t type_class;
     jsize       n;
     htri_t      vl_data_class;
-    herr_t      status = FAIL;
-    jboolean    readBufIsCopy;
+    herr_t      status  = FAIL;
     jbyteArray *readBuf = NULL;
 
     UNUSED(clss);
@@ -1107,7 +1106,6 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
         jobject    *jList  = NULL;
 
         size_t i, j, x;
-        char  *cp_vp = NULL;
 
         if (!(typeSize = H5Tget_size(mem_type_id)))
             H5_LIBRARY_ERROR(ENVONLY);
@@ -1127,7 +1125,7 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
             H5_LIBRARY_ERROR(ENVONLY);
 
         /* Cache class types */
-        jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
+        /* jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
         jclass cByte   = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
         jclass cShort  = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
         jclass cInt    = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
@@ -1135,8 +1133,10 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
         jclass cFloat  = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
         jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
 
+        /*
         jmethodID boolValueMid =
             ENVPTR->GetStaticMethodID(ENVONLY, cBool, "valueOf", "(Z)Ljava/lang/Boolean;");
+        */
         jmethodID byteValueMid = ENVPTR->GetStaticMethodID(ENVONLY, cByte, "valueOf", "(B)Ljava/lang/Byte;");
         jmethodID shortValueMid =
             ENVPTR->GetStaticMethodID(ENVONLY, cShort, "valueOf", "(S)Ljava/lang/Short;");
@@ -1153,21 +1153,28 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
 
         /* Convert each element to a list */
         for (i = 0; i < (size_t)n; i++) {
+            hvl_t vl_elem;
+
             // The list we're going to return:
             if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
                 CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
-            cp_vp = (char *)rawBuf + i * typeSize;
             /* Get the number of sequence elements */
-            jsize nelmts = ((hvl_t *)cp_vp)->len;
+            HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
+
+            jsize nelmts = (jsize)vl_elem.len;
+            if (vl_elem.len != (size_t)nelmts)
+                H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of number of VL elements");
+            if (nelmts < 0)
+                H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DreadVL: number of VL elements < 0");
 
             jobject jobj = NULL;
-            for (j = 0; j < nelmts; j++) {
+            for (j = 0; j < (size_t)nelmts; j++) {
                 switch (vlClass) {
                     /*case H5T_BOOL: {
                         jboolean boolValue;
-                        for (x = 0; x < (int)vlSize; x++) {
-                            ((char *)&boolValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j*vlSize+x];
+                        for (x = 0; x < vlSize; x++) {
+                            ((char *)&boolValue)[x] = ((char *)vl_elem.p)[j*vlSize+x];
                         }
 
                         jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cBool, boolValueMid, boolValue);
@@ -1178,8 +1185,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                         switch (vlSize) {
                             case sizeof(jbyte): {
                                 jbyte byteValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&byteValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&byteValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj =
@@ -1189,8 +1196,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                             }
                             case sizeof(jshort): {
                                 jshort shortValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&shortValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&shortValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cShort, shortValueMid,
@@ -1200,8 +1207,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                             }
                             case sizeof(jint): {
                                 jint intValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&intValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&intValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cInt, intValueMid, intValue);
@@ -1210,8 +1217,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                             }
                             case sizeof(jlong): {
                                 jlong longValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&longValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&longValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj =
@@ -1226,8 +1233,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                         switch (vlSize) {
                             case sizeof(jfloat): {
                                 jfloat floatValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&floatValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&floatValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
@@ -1237,8 +1244,8 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                             }
                             case sizeof(jdouble): {
                                 jdouble doubleValue;
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)&doubleValue)[x] = ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)&doubleValue)[x] = ((char *)vl_elem.p)[j * vlSize + x];
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cDouble, doubleValueMid,
@@ -1252,14 +1259,19 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                     case H5T_REFERENCE: {
                         jboolean bb;
                         jbyte   *barray = NULL;
-                        if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, vlSize)))
+
+                        jsize byteArraySize = (jsize)vlSize;
+                        if (vlSize != (size_t)byteArraySize)
+                            H5_JNI_FATAL_ERROR(ENVONLY, "H5DreadVL: overflow of byteArraySize");
+
+                        if (NULL == (jobj = ENVPTR->NewByteArray(ENVONLY, byteArraySize)))
                             CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
                         PIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, &bb,
                                        "readVL reference: byte array not pinned");
 
-                        for (x = 0; x < (int)vlSize; x++) {
-                            barray[x] = ((jbyte *)((hvl_t *)cp_vp)->p)[j * vlSize + x];
+                        for (x = 0; x < vlSize; x++) {
+                            barray[x] = ((jbyte *)vl_elem.p)[j * vlSize + x];
                         }
                         if (barray)
                             UNPIN_BYTE_ARRAY(ENVONLY, (jbyteArray)jobj, barray, jobj ? 0 : JNI_ABORT);
@@ -1337,7 +1349,6 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
         jobject    *jList  = NULL;
 
         size_t i, j, x;
-        char  *cp_vp = NULL;
 
         if (!(typeSize = H5Tget_size(mem_type_id)))
             H5_LIBRARY_ERROR(ENVONLY);
@@ -1353,7 +1364,7 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
             H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate raw VL write buffer");
 
         /* Cache class types */
-        jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean");
+        /* jclass cBool   = ENVPTR->FindClass(ENVONLY, "java/lang/Boolean"); */
         jclass cByte   = ENVPTR->FindClass(ENVONLY, "java/lang/Byte");
         jclass cShort  = ENVPTR->FindClass(ENVONLY, "java/lang/Short");
         jclass cInt    = ENVPTR->FindClass(ENVONLY, "java/lang/Integer");
@@ -1361,7 +1372,7 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
         jclass cFloat  = ENVPTR->FindClass(ENVONLY, "java/lang/Float");
         jclass cDouble = ENVPTR->FindClass(ENVONLY, "java/lang/Double");
 
-        jmethodID boolValueMid   = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z");
+        /* jmethodID boolValueMid   = ENVPTR->GetMethodID(ENVONLY, cBool, "booleanValue", "()Z"); */
         jmethodID byteValueMid   = ENVPTR->GetMethodID(ENVONLY, cByte, "byteValue", "()B");
         jmethodID shortValueMid  = ENVPTR->GetMethodID(ENVONLY, cShort, "shortValue", "()S");
         jmethodID intValueMid    = ENVPTR->GetMethodID(ENVONLY, cInt, "intValue", "()I");
@@ -1371,6 +1382,8 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
 
         /* Convert each list to a vlen element */
         for (i = 0; i < (size_t)n; i++) {
+            hvl_t vl_elem;
+
             if (NULL == (jList = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)buf, (jsize)i)))
                 CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
@@ -1384,21 +1397,25 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
             jobjectArray array   = (jobjectArray)ENVPTR->CallObjectMethod(ENVONLY, jList, mToArray);
             jsize        jnelmts = ENVPTR->GetArrayLength(ENVONLY, array);
 
-            cp_vp                 = (char *)rawBuf + i * typeSize;
-            ((hvl_t *)cp_vp)->len = jnelmts;
+            if (jnelmts < 0)
+                H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5DwriteVL: number of VL elements < 0");
+
+            HDmemcpy(&vl_elem, (char *)rawBuf + i * typeSize, sizeof(hvl_t));
+            vl_elem.len = (size_t)jnelmts;
 
-            if (NULL == (((hvl_t *)cp_vp)->p = HDmalloc(jnelmts * vlSize)))
+            if (NULL == (vl_elem.p = HDmalloc((size_t)jnelmts * vlSize)))
                 H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DwriteVL: failed to allocate vlen ptr buffer");
+
             jobject jobj = NULL;
-            for (j = 0; j < (int)jnelmts; j++) {
+            for (j = 0; j < (size_t)jnelmts; j++) {
                 if (NULL == (jobj = ENVPTR->GetObjectArrayElement(ENVONLY, (jobjectArray)array, (jsize)j)))
                     CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
 
                 switch (vlClass) {
                     /* case H5T_BOOL: {
                             jboolean boolValue = ENVPTR->CallBooleanMethod(ENVONLY, jobj, boolValueMid);
-                            for (x = 0; x < (int)vlSize; x++) {
-                                ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&boolValue)[x];
+                            for (x = 0; x < vlSize; x++) {
+                                ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&boolValue)[x];
                             }
                             break;
                     } */
@@ -1406,29 +1423,29 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                         switch (vlSize) {
                             case sizeof(jbyte): {
                                 jbyte byteValue = ENVPTR->CallByteMethod(ENVONLY, jobj, byteValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&byteValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&byteValue)[x];
                                 }
                                 break;
                             }
                             case sizeof(jshort): {
                                 jshort shortValue = ENVPTR->CallShortMethod(ENVONLY, jobj, shortValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&shortValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&shortValue)[x];
                                 }
                                 break;
                             }
                             case sizeof(jint): {
                                 jint intValue = ENVPTR->CallIntMethod(ENVONLY, jobj, intValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&intValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&intValue)[x];
                                 }
                                 break;
                             }
                             case sizeof(jlong): {
                                 jlong longValue = ENVPTR->CallLongMethod(ENVONLY, jobj, longValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&longValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&longValue)[x];
                                 }
                                 break;
                             }
@@ -1439,15 +1456,15 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                         switch (vlSize) {
                             case sizeof(jfloat): {
                                 jfloat floatValue = ENVPTR->CallFloatMethod(ENVONLY, jobj, floatValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&floatValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&floatValue)[x];
                                 }
                                 break;
                             }
                             case sizeof(jdouble): {
                                 jdouble doubleValue = ENVPTR->CallDoubleMethod(ENVONLY, jobj, doubleValueMid);
-                                for (x = 0; x < (int)vlSize; x++) {
-                                    ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)&doubleValue)[x];
+                                for (x = 0; x < vlSize; x++) {
+                                    ((char *)vl_elem.p)[j * vlSize + x] = ((char *)&doubleValue)[x];
                                 }
                                 break;
                             }
@@ -1456,8 +1473,8 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                     }
                     case H5T_REFERENCE: {
                         jbyte *barray = (jbyte *)ENVPTR->GetByteArrayElements(ENVONLY, jobj, 0);
-                        for (x = 0; x < (int)vlSize; x++) {
-                            ((char *)((hvl_t *)cp_vp)->p)[j * vlSize + x] = ((char *)barray)[x];
+                        for (x = 0; x < vlSize; x++) {
+                            ((char *)vl_elem.p)[j * vlSize + x] = ((char *)barray)[x];
                         }
                         ENVPTR->ReleaseByteArrayElements(ENVONLY, jobj, barray, 0);
                         break;
@@ -1468,6 +1485,9 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                 }
                 ENVPTR->DeleteLocalRef(ENVONLY, jobj);
             }
+
+            HDmemcpy((char *)rawBuf + i * typeSize, &vl_elem, sizeof(hvl_t));
+
             ENVPTR->DeleteLocalRef(ENVONLY, jList);
         } /* end for (i = 0; i < n; i++) */
 
diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c
index 54f4a01..763be05 100644
--- a/java/src/jni/h5rImp.c
+++ b/java/src/jni/h5rImp.c
@@ -312,7 +312,7 @@ Java_hdf_hdf5lib_H5_H5Rget_1name_1string(JNIEnv *env, jclass clss, jlong loc_id,
                                          jbyteArray ref)
 {
     jboolean isCopy;
-    jstring  str;
+    jstring  str = NULL;
     jsize    refBufLen;
     jbyte   *refBuf   = NULL;
     char    *aName    = NULL;
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 1e69428..5344d18 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -650,10 +650,8 @@ done:
 int
 h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *ref_buf)
 {
-    hid_t region = H5I_INVALID_HID;
-    char  ref_name[1024];
-
-    int ret_value = FAIL;
+    char ref_name[1024];
+    int  ret_value = FAIL;
 
     if ((H5Rget_name(region_obj, H5R_DATASET_REGION, ref_buf, (char *)ref_name, 1024)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
@@ -661,8 +659,8 @@ h5str_sprint_reference(JNIEnv *env, h5str_t *out_str, hid_t region_obj, void *re
         H5_ASSERTION_ERROR(ENVONLY, "Unable to append string.");
 
     ret_value = SUCCEED;
-done:
 
+done:
     return ret_value;
 } /* h5str_sprint_reference */
 
@@ -2132,14 +2130,15 @@ h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hs
             }
 
             for (block_index = 0; block_index < block_nelmts; block_index++) {
-                mem = ((unsigned char *)_mem) + block_index * size;
+                hvl_t vl_elem;
+
+                HDmemcpy(&vl_elem, ((unsigned char *)_mem) + block_index * size, sizeof(hvl_t));
 
                 /* Get the number of sequence elements */
-                nelmts = ((hvl_t *)mem)->len;
+                nelmts = vl_elem.len;
 
                 /* dump the array element */
-                if (h5str_render_bin_output(stream, container, memb, ((char *)(((hvl_t *)mem)->p)), nelmts) <
-                    0) {
+                if (h5str_render_bin_output(stream, container, memb, ((char *)(vl_elem.p)), nelmts) < 0) {
                     ret_value = FAIL;
                     break;
                 }
@@ -2563,8 +2562,8 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
     int     carry; /* counter carry value */
 
     /* Print info */
-    hsize_t p_nelmts;      /* total selected elmts */
-    size_t  p_type_nbytes; /* size of memory type */
+    hssize_t p_nelmts;      /* total selected elmts */
+    size_t   p_type_nbytes; /* size of memory type */
 
     /* Stripmine info */
     unsigned char *sm_buf = NULL;              /* buffer for raw data */
@@ -2758,7 +2757,7 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
     int      ndims;                    /* rank of dataspace */
     unsigned i;                        /* counters  */
     hsize_t  total_size[H5S_MAX_RANK]; /* total size of dataset*/
-    hsize_t  p_nelmts;                 /* total selected elmts */
+    hssize_t p_nelmts;                 /* total selected elmts */
 
     unsigned char *sm_buf = NULL;         /* buffer for raw data */
     hsize_t        sm_size[H5S_MAX_RANK]; /* stripmine size */