Fix Java JNI warnings (#4229)

java/src/jni/h5aImp.c

@@ -1107,12 +1107,12 @@ Java_hdf_hdf5lib_H5_H5Awrite_1string(JNIEnv *env, jclass clss, jlong attr_id, jl
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
 {
- jbyte *readBuf = NULL;
+ void  *readBuf = NULL;
  hsize_t dims[H5S_MAX_RANK];
  hid_t sid = H5I_INVALID_HID;
  size_t typeSize;
  H5T_class_t type_class;
- jsize vl_array_len;
+ jsize vl_array_len = 0;
  htri_t vl_data_class;
  herr_t status = FAIL;
  htri_t is_variable = 0;
@@ -1136,7 +1136,7 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
  if (NULL == (readBuf = calloc((size_t)vl_array_len, typeSize)))
  H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Aread: failed to allocate raw VL read buffer");
 
- if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, (void *)readBuf)) < 0)
+ if ((status = H5Aread((hid_t)attr_id, (hid_t)mem_type_id, readBuf)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
  if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
@@ -1173,12 +1173,12 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem_type_id, jobjectArray buf)
 {
- jbyte *writeBuf = NULL;
+ void  *writeBuf = NULL;
  hsize_t dims[H5S_MAX_RANK];
  hid_t sid = H5I_INVALID_HID;
  size_t typeSize;
  H5T_class_t type_class;
- jsize vl_array_len;
+ jsize vl_array_len = 0;
  htri_t vl_data_class;
  herr_t status = FAIL;
  htri_t is_variable = 0;

java/src/jni/h5dImp.c

@@ -185,7 +185,7 @@ Java_hdf_hdf5lib_H5_H5Dread(JNIEnv *env, jclass clss, jlong dataset_id, jlong me
  jbyte *readBuf = NULL;
  size_t typeSize;
  H5T_class_t type_class;
- jsize vl_array_len; // Only used by vl_data_class types
+ jsize vl_array_len = 0; // Only used by vl_data_class types
  htri_t vl_data_class;
  herr_t status = FAIL;
 
@@ -266,7 +266,7 @@ Java_hdf_hdf5lib_H5_H5Dwrite(JNIEnv *env, jclass clss, jlong dataset_id, jlong m
  jbyte *writeBuf = NULL;
  size_t typeSize;
  H5T_class_t type_class;
- jsize vl_array_len; // Only used by vl_data_class types
+ jsize vl_array_len = 0; // Only used by vl_data_class types
  htri_t vl_data_class;
  herr_t status = FAIL;
 
@@ -1134,7 +1134,7 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
  jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
 {
- jbyte *readBuf = NULL;
+ void  *readBuf = NULL;
  size_t typeSize;
  H5T_class_t type_class;
  jsize vl_array_len;
@@ -1164,7 +1164,7 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
  H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5DreadVL: failed to allocate raw VL read buffer");
 
  if ((status = H5Dread((hid_t)dataset_id, (hid_t)mem_type_id, (hid_t)mem_space_id, (hid_t)file_space_id,
- (hid_t)xfer_plist_id, (void *)readBuf)) < 0)
+ (hid_t)xfer_plist_id, readBuf)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
  if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
@@ -1194,7 +1194,7 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id,
  jlong mem_space_id, jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
 {
- jbyte *writeBuf = NULL;
+ void  *writeBuf = NULL;
  size_t typeSize;
  H5T_class_t type_class;
  jsize vl_array_len; // Only used by vl_data_class types

java/src/jni/h5eImp.c

@@ -455,7 +455,7 @@ Java_hdf_hdf5lib_H5_H5Eget_1msg(JNIEnv *env, jclass clss, jlong msg_id, jintArra
  H5_LIBRARY_ERROR(ENVONLY);
  namePtr[buf_size] = '\0';
 
- theArray[0] = error_msg_type;
+ theArray[0] = (jint)error_msg_type;
 
  if (NULL == (str = ENVPTR->NewStringUTF(ENVONLY, namePtr)))
  CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);

java/src/jni/h5pDCPLImp.c

@@ -77,13 +77,11 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5Pset_1chunk(JNIEnv *env, jclass clss, jlong plist, jint ndims, jbyteArray dim)
 {
  jboolean isCopy;
- hsize_t *da = NULL;
- hsize_t *lp = NULL;
- size_t i;
+ hsize_t *chunk_dims = NULL;
+ uint8_t *theArray_p = NULL;
  size_t rank;
  jsize arrLen;
  jbyte *theArray = NULL;
- jlong *jlp = NULL;
  herr_t status = FAIL;
 
  UNUSED(clss);
@@ -104,22 +102,29 @@ Java_hdf_hdf5lib_H5_H5Pset_1chunk(JNIEnv *env, jclass clss, jlong plist, jint nd
 
  PIN_BYTE_ARRAY(ENVONLY, dim, theArray, &isCopy, "H5Pset_chunk: dim array not pinned");
 
- if (NULL == (da = lp = (hsize_t *)malloc(rank * sizeof(hsize_t))))
+ if (NULL == (chunk_dims = malloc(rank * sizeof(hsize_t))))
  H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pset_chunk: memory allocation failed");
 
- jlp = (jlong *)theArray;
- for (i = 0; i < rank; i++) {
- *lp = (hsize_t)*jlp;
- lp++;
- jlp++;
- } /* end if */
+ theArray_p = (uint8_t *)theArray;
+ for (size_t i = 0; i < rank; i++) {
+ jlong dim_val;
 
- if ((status = H5Pset_chunk((hid_t)plist, (int)ndims, da)) < 0)
+ memcpy(&dim_val, theArray_p, sizeof(jlong));
+
+ if (dim_val < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Pset_chunk: chunk dimensions can't be negative");
+
+ chunk_dims[i] = (hsize_t)dim_val;
+
+ theArray_p += sizeof(jlong);
+ }
+
+ if ((status = H5Pset_chunk((hid_t)plist, (int)ndims, chunk_dims)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
 
 done:
- if (da)
- free(da);
+ free(chunk_dims);
+
  if (theArray)
  UNPIN_BYTE_ARRAY(ENVONLY, dim, theArray, JNI_ABORT);
 

java/src/jni/h5pFAPLImp.c

@@ -1741,15 +1741,15 @@ Java_hdf_hdf5lib_H5_H5Pget_1mdc_1config(JNIEnv *env, jclass clss, jlong plist)
  args[9].j = (jlong)cacheinfo.max_size;
  args[10].j = (jlong)cacheinfo.min_size;
  args[11].j = cacheinfo.epoch_length;
- args[12].i = cacheinfo.incr_mode;
+ args[12].i = (jint)cacheinfo.incr_mode;
  args[13].d = cacheinfo.lower_hr_threshold;
  args[14].d = cacheinfo.increment;
  args[15].z = cacheinfo.apply_max_increment;
  args[16].j = (jlong)cacheinfo.max_increment;
- args[17].i = cacheinfo.flash_incr_mode;
+ args[17].i = (jint)cacheinfo.flash_incr_mode;
  args[18].d = cacheinfo.flash_multiple;
  args[19].d = cacheinfo.flash_threshold;
- args[20].i = cacheinfo.decr_mode;
+ args[20].i = (jint)cacheinfo.decr_mode;
  args[21].d = cacheinfo.upper_hr_threshold;
  args[22].d = cacheinfo.decrement;
  args[23].z = cacheinfo.apply_max_decrement;

java/src/jni/h5rImp.c

@@ -204,6 +204,12 @@ Java_hdf_hdf5lib_H5_H5Rdestroy(JNIEnv *env, jclass clss, jbyteArray ref)
  if ((status = H5Rdestroy(&loc_ref)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
 
+ /* Reset buffer to 0 to be safe. H5Rdestroy does this, but
+ * only on our temporary reference object that we copied
+ * into for alignment reasons.
+ */
+ memset(refBuf, 0, H5R_REF_BUF_SIZE);
+
 done:
  if (refBuf)
  UNPIN_BYTE_ARRAY(ENVONLY, ref, refBuf, (status < 0) ? JNI_ABORT : 0);

java/src/jni/h5sImp.c

@@ -221,49 +221,52 @@ Java_hdf_hdf5lib_H5_H5Sselect_1elements(JNIEnv *env, jclass clss, jlong space_id
  jbyteArray coords)
 {
  jboolean isCopy;
- hsize_t *lp = NULL;
- hsize_t *llp = NULL;
- jlong *jlp = NULL;
- jbyte *P = NULL;
+ hsize_t *coords_p = NULL;
+ uint8_t *pinned_arr_p = NULL;
+ jbyte *pinned_arr = NULL;
  jsize size;
- int ii;
- int nlongs;
+ size_t nlongs;
  herr_t status = FAIL;
 
  UNUSED(clss);
 
  if (NULL == coords)
  H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5Sselect_elements: coords is NULL");
 
- PIN_BYTE_ARRAY(ENVONLY, coords, P, &isCopy, "H5Sselect_elements: coords not pinned");
+ PIN_BYTE_ARRAY(ENVONLY, coords, pinned_arr, &isCopy, "H5Sselect_elements: coords not pinned");
 
  if ((size = ENVPTR->GetArrayLength(ENVONLY, coords)) < 0) {
  CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
  H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_elements: coords array length < 0");
  }
 
- nlongs = (int)((size_t)size / sizeof(jlong));
+ nlongs = (size_t)size / sizeof(jlong);
 
- if (NULL == (lp = (hsize_t *)malloc((size_t)nlongs * sizeof(hsize_t))))
+ if (NULL == (coords_p = malloc(nlongs * sizeof(hsize_t))))
  H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Sselect_elements: failed to allocate coordinate buffer");
 
- jlp = (jlong *)P;
- llp = lp;
- for (ii = 0; ii < nlongs; ii++) {
- *lp = (hsize_t)*jlp;
- lp++;
- jlp++;
- } /* end for */
+ pinned_arr_p = (uint8_t *)pinned_arr;
+ for (size_t i = 0; i < nlongs; i++) {
+ jlong coord_elem;
+
+ memcpy(&coord_elem, pinned_arr_p, sizeof(jlong));
+
+ if (coord_elem < 0)
+ H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Sselect_elements: coordinate element can't be negative");
 
- if ((status = H5Sselect_elements(space_id, (H5S_seloper_t)op, (size_t)num_elemn, (const hsize_t *)llp)) <
- 0)
+ coords_p[i] = (hsize_t)coord_elem;
+
+ pinned_arr_p += sizeof(jlong);
+ }
+
+ if ((status = H5Sselect_elements(space_id, (H5S_seloper_t)op, (size_t)num_elemn, coords_p)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
 
 done:
- if (llp)
- free(llp);
- if (P)
- UNPIN_BYTE_ARRAY(ENVONLY, coords, P, JNI_ABORT);
+ free(coords_p);
+
+ if (pinned_arr)
+ UNPIN_BYTE_ARRAY(ENVONLY, coords, pinned_arr, JNI_ABORT);
 
  return (jint)status;
 } /* end Java_hdf_hdf5lib_H5_H5Sselect_1elements */
@@ -630,49 +633,49 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_H5_H5Soffset_1simple(JNIEnv *env, jclass clss, jlong space_id, jbyteArray offset)
 {
  jboolean isCopy;
- hssize_t *sa = NULL;
- hssize_t *lp = NULL;
+ hssize_t *offset_dims = NULL;
+ uint8_t *pinned_arr_p = NULL;
+ jbyte *pinned_arr = NULL;
  size_t rank;
- jsize i;
- jbyte *P = NULL;
- jlong *jlp = NULL;
  herr_t status = FAIL;
 
  UNUSED(clss);
 
  if (NULL != offset) {
- PIN_BYTE_ARRAY(ENVONLY, offset, P, &isCopy, "H5Soffset_simple: offset not pinned");
+ jsize size;
+
+ PIN_BYTE_ARRAY(ENVONLY, offset, pinned_arr, &isCopy, "H5Soffset_simple: offset not pinned");
 
- if ((i = ENVPTR->GetArrayLength(ENVONLY, offset)) < 0) {
+ if ((size = ENVPTR->GetArrayLength(ENVONLY, offset)) < 0) {
  CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
  H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Soffset_simple: offset array length < 0");
  }
 
- rank = (size_t)i / sizeof(jlong);
+ rank = (size_t)size / sizeof(jlong);
 
- if (NULL == (sa = lp = (hssize_t *)malloc((size_t)rank * sizeof(hssize_t))))
+ if (NULL == (offset_dims = malloc((size_t)rank * sizeof(hssize_t))))
  H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Soffset_simple: failed to allocate offset buffer");
 
- jlp = (jlong *)P;
- for (i = 0; (size_t)i < rank; i++) {
- *lp = (hssize_t)*jlp;
- lp++;
- jlp++;
- } /* end for */
- }
- else {
- P = NULL;
- sa = (hssize_t *)P;
+ pinned_arr_p = (uint8_t *)pinned_arr;
+ for (size_t i = 0; i < rank; i++) {
+ jlong offset_elem;
+
+ memcpy(&offset_elem, pinned_arr_p, sizeof(jlong));
+
+  offset_dims[i] = (hssize_t)offset_elem;
+
+  pinned_arr_p += sizeof(jlong);
+ }
  }
 
- if ((status = H5Soffset_simple(space_id, sa)) < 0)
+ if ((status = H5Soffset_simple(space_id, offset_dims)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
 
 done:
- if (sa)
- free(sa);
- if (P)
- UNPIN_BYTE_ARRAY(ENVONLY, offset, P, JNI_ABORT);
+ free(offset_dims);
+
+ if (pinned_arr)
+ UNPIN_BYTE_ARRAY(ENVONLY, offset, pinned_arr, JNI_ABORT);
 
  return (jint)status;
 } /* end Java_hdf_hdf5lib_H5_H5Soffset_1simple */

java/src/jni/h5tImp.c

@@ -447,8 +447,13 @@ Java_hdf_hdf5lib_H5_H5Tget_1fields_1int(JNIEnv *env, jclass clss, jlong type_id,
 {
  jboolean isCopy;
  jsize arrLen;
- jint *P = NULL;
- herr_t status = FAIL;
+ size_t spos;
+ size_t epos;
+ size_t esize;
+ size_t mpos;
+ size_t msize;
+ jint *pinned_arr = NULL;
+ herr_t status = FAIL;
 
  UNUSED(clss);
 
@@ -462,15 +467,20 @@ Java_hdf_hdf5lib_H5_H5Tget_1fields_1int(JNIEnv *env, jclass clss, jlong type_id,
  if (arrLen < 5)
  H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Tget_fields_int: fields input array < order 5");
 
- PIN_INT_ARRAY(ENVONLY, fields, P, &isCopy, "H5Tget_fields_int: fields not pinned");
+ PIN_INT_ARRAY(ENVONLY, fields, pinned_arr, &isCopy, "H5Tget_fields_int: fields not pinned");
 
- if ((status = H5Tget_fields((hid_t)type_id, (size_t *)&(P[0]), (size_t *)&(P[1]), (size_t *)&(P[2]),
- (size_t *)&(P[3]), (size_t *)&(P[4]))) < 0)
+ if ((status = H5Tget_fields((hid_t)type_id, &spos, &epos, &esize, &mpos, &msize)) < 0)
  H5_LIBRARY_ERROR(ENVONLY);
 
+ pinned_arr[0] = (jint)spos;
+ pinned_arr[1] = (jint)epos;
+ pinned_arr[2] = (jint)esize;
+ pinned_arr[3] = (jint)mpos;
+ pinned_arr[4] = (jint)msize;
+
 done:
- if (P)
- UNPIN_INT_ARRAY(ENVONLY, fields, P, (status < 0) ? JNI_ABORT : 0);
+ if (pinned_arr)
+ UNPIN_INT_ARRAY(ENVONLY, fields, pinned_arr, (status < 0) ? JNI_ABORT : 0);
 
  return (jint)status;
 } /* end Java_hdf_hdf5lib_H5_H5Tget_1fields_1int */