Fix mostly java warnings, and cpp cast (#2134)

7 files changed, 198 insertions, 181 deletions

diff --git a/java/src/jni/h5aImp.c b/java/src/jni/h5aImp.c
index e5e8462..086fea8 100644
--- a/java/src/jni/h5aImp.c
+++ b/java/src/jni/h5aImp.c
@@ -1084,7 +1084,7 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
         /* Get size of data array */
         if ((n = ENVPTR->GetArrayLength(ENVONLY, buf)) < 0) {
             CHECK_JNI_EXCEPTION(ENVONLY, JNI_TRUE);
-            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5Aread: readBuf length < 0");
+            H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5AreadVL: readBuf length < 0");
         }
 
         dims[0] = (hsize_t)n;
@@ -1095,12 +1095,12 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
     if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
     if (type_class == H5T_VLEN) {
-        size_t      typeSize;
-        hid_t       memb = H5I_INVALID_HID;
-        H5T_class_t vlClass;
-        size_t      vlSize;
-        void       *rawBuf = NULL;
-        jobject    *jList  = NULL;
+        size_t       typeSize;
+        hid_t        memb = H5I_INVALID_HID;
+        H5T_class_t  vlClass;
+        size_t       vlSize;
+        void        *rawBuf = NULL;
+        jobjectArray jList  = NULL;
 
         size_t i, j, x;
 
@@ -1234,7 +1234,7 @@ Java_hdf_hdf5lib_H5_H5AreadVL(JNIEnv *env, jclass clss, jlong attr_id, jlong mem
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
-                                                                      floatValue);
+                                                                      (double)floatValue);
                                 CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
                                 break;
                             }
@@ -1321,7 +1321,7 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
     htri_t      vl_data_class;
     herr_t      status = FAIL;
     jboolean    writeBufIsCopy;
-    jbyteArray *writeBuf = NULL;
+    jbyteArray  writeBuf = NULL;
 
     UNUSED(clss);
 
@@ -1344,12 +1344,12 @@ Java_hdf_hdf5lib_H5_H5AwriteVL(JNIEnv *env, jclass clss, jlong attr_id, jlong me
     if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
     if (type_class == H5T_VLEN) {
-        size_t      typeSize;
-        hid_t       memb = H5I_INVALID_HID;
-        H5T_class_t vlClass;
-        size_t      vlSize;
-        void       *rawBuf = NULL;
-        jobject    *jList  = NULL;
+        size_t       typeSize;
+        hid_t        memb = H5I_INVALID_HID;
+        H5T_class_t  vlClass;
+        size_t       vlSize;
+        void        *rawBuf = NULL;
+        jobjectArray jList  = NULL;
 
         size_t i, j, x;
 
diff --git a/java/src/jni/h5dImp.c b/java/src/jni/h5dImp.c
index e6e9a76..59775e3 100644
--- a/java/src/jni/h5dImp.c
+++ b/java/src/jni/h5dImp.c
@@ -1110,12 +1110,12 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
     if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
     if (type_class == H5T_VLEN) {
-        size_t      typeSize;
-        hid_t       memb = H5I_INVALID_HID;
-        H5T_class_t vlClass;
-        size_t      vlSize;
-        void       *rawBuf = NULL;
-        jobject    *jList  = NULL;
+        size_t       typeSize;
+        hid_t        memb = H5I_INVALID_HID;
+        H5T_class_t  vlClass;
+        size_t       vlSize;
+        void        *rawBuf = NULL;
+        jobjectArray jList  = NULL;
 
         size_t i, j, x;
 
@@ -1250,7 +1250,7 @@ Java_hdf_hdf5lib_H5_H5DreadVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
                                 }
 
                                 jobj = ENVPTR->CallStaticObjectMethod(ENVONLY, cFloat, floatValueMid,
-                                                                      floatValue);
+                                                                      (double)floatValue);
                                 CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
                                 break;
                             }
@@ -1334,7 +1334,7 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
     htri_t      vl_data_class;
     herr_t      status = FAIL;
     jboolean    writeBufIsCopy;
-    jbyteArray *writeBuf = NULL;
+    jbyteArray  writeBuf = NULL;
 
     UNUSED(clss);
 
@@ -1353,12 +1353,12 @@ Java_hdf_hdf5lib_H5_H5DwriteVL(JNIEnv *env, jclass clss, jlong dataset_id, jlong
     if ((type_class = H5Tget_class((hid_t)mem_type_id)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
     if (type_class == H5T_VLEN) {
-        size_t      typeSize;
-        hid_t       memb = H5I_INVALID_HID;
-        H5T_class_t vlClass;
-        size_t      vlSize;
-        void       *rawBuf = NULL;
-        jobject    *jList  = NULL;
+        size_t       typeSize;
+        hid_t        memb = H5I_INVALID_HID;
+        H5T_class_t  vlClass;
+        size_t       vlSize;
+        void        *rawBuf = NULL;
+        jobjectArray jList  = NULL;
 
         size_t i, j, x;
 
diff --git a/java/src/jni/h5jni.h b/java/src/jni/h5jni.h
index 2c93846..5af5a91 100644
--- a/java/src/jni/h5jni.h
+++ b/java/src/jni/h5jni.h
@@ -257,6 +257,23 @@
     do {                                                                                                     \
         (*envptr)->ReleaseStringUTFChars(envptr, pinnedString, stringToRelease);                             \
     } while (0)
+/*
+ * Above String macros may be incorrect, suggested code for getting a cstr from java
+ * int jstr_to_cstr(JNIEnv *jenv, jstring j_str, char *c_str, size_t cstr_len)
+ * {
+ *     int32_t j_len, c_len;
+ *
+ *     c_len = (*jenv)->GetStringUTFLength(jenv, j_str);
+ *     if (c_len > (int32_t)cstr_len)
+ *         return -ENAMETOOLONG;
+ *     j_len = (*jenv)->GetStringLength(jenv, j_str);
+ *     (*jenv)->GetStringUTFRegion(jenv, j_str, 0, j_len, c_str);
+ *     if ((*jenv)->ExceptionCheck(jenv))
+ *         return -EIO;
+ *     return 0;
+ * }
+ *
+ */
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index e8417b6..37d0194 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -436,7 +436,7 @@ h5str_convert(JNIEnv *env, char **in_str, hid_t container, hid_t tid, void *out_
             break;
 
         case H5T_ENUM: {
-            void *value;
+            void *value = NULL;
 
             token = HDstrtok(this_str, delimiter);
 
@@ -865,7 +865,7 @@ h5str_sprintf(JNIEnv *env, h5str_t *out_str, hid_t container, hid_t tid, void *i
                     if (NULL == (this_str = (char *)HDmalloc(this_len)))
                         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_sprintf: failed to allocate string buffer");
 
-                    if (HDsnprintf(this_str, this_len, "%g", tmp_float) < 0)
+                    if (HDsnprintf(this_str, this_len, "%g", (double)tmp_float) < 0)
                         H5_JNI_FATAL_ERROR(ENVONLY, "h5str_sprintf: HDsnprintf failure");
 
                     break;
@@ -2273,10 +2273,10 @@ h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hs
         }
 
         case H5T_STRING: {
-            unsigned char tempuchar;
             unsigned int  i;
             H5T_str_t     pad;
-            char         *s;
+            char         *s = NULL;
+            unsigned char tempuchar;
 
             if ((pad = H5Tget_strpad(tid)) < 0) {
                 ret_value = FAIL;
@@ -2287,7 +2287,7 @@ h5str_render_bin_output(FILE *stream, hid_t container, hid_t tid, void *_mem, hs
                 mem = ((unsigned char *)_mem) + block_index * size;
 
                 if (H5Tis_variable_str(tid)) {
-                    s = *(char **)mem;
+                    s = *(char **)((void *)mem);
                     if (s != NULL)
                         size = HDstrlen(s);
                 }
@@ -2919,24 +2919,20 @@ done:
 int
 h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
 {
+    hid_t   f_space = H5I_INVALID_HID; /* file data space */
     hsize_t elmtno;                    /* counter  */
+    size_t  i = 0;                     /* counter  */
+    int     sndims;                    /* rank of dataspace */
+    int     carry;                     /* counter carry value */
     hsize_t zero[8];                   /* vector of zeros */
     hsize_t total_size[H5S_MAX_RANK];  /* total size of dataset*/
-    size_t  i;                         /* counter  */
-    hid_t   f_space = H5I_INVALID_HID; /* file data space */
-    int     ndims;
-    int     carry; /* counter carry value */
-
-    /* Print info */
-    hssize_t p_nelmts;      /* total selected elmts */
-    size_t   p_type_nbytes; /* size of memory type */
 
     /* Stripmine info */
-    void   *sm_buf = NULL;              /* buffer for raw data */
-    hsize_t sm_size[H5S_MAX_RANK];      /* stripmine size */
-    hsize_t sm_nbytes;                  /* bytes per stripmine */
-    hsize_t sm_nelmts;                  /* elements per stripmine */
-    hid_t   sm_space = H5I_INVALID_HID; /* stripmine data space */
+    hsize_t        sm_size[H5S_MAX_RANK];      /* stripmine size */
+    hsize_t        sm_nbytes;                  /* bytes per stripmine */
+    hsize_t        sm_nelmts;                  /* elements per stripmine */
+    unsigned char *sm_buf   = NULL;            /* buffer for raw data */
+    hid_t          sm_space = H5I_INVALID_HID; /* stripmine data space */
 
     /* Hyperslab info */
     hsize_t hs_offset[H5S_MAX_RANK]; /* starting offset */
@@ -2944,11 +2940,11 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
     hsize_t hs_nelmts;               /* elements in request */
 
     /* VL data special information */
-    unsigned int vl_data = 0; /* contains VL datatypes */
-    hid_t        p_type  = H5I_INVALID_HID;
-    hid_t        f_type  = H5I_INVALID_HID;
+    unsigned int vl_data   = 0; /* contains VL datatypes */
+    int          ret_value = FAIL;
 
-    int ret_value = FAIL;
+    hid_t p_type = H5I_INVALID_HID;
+    hid_t f_type = H5I_INVALID_HID;
 
     if (dset < 0)
         H5_BAD_ARGUMENT_ERROR(ENVONLY, "h5str_dump_simple_dset: dset ID < 0");
@@ -2959,18 +2955,21 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
     if ((f_space = H5Dget_space(dset)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0)
+    if ((sndims = H5Sget_simple_extent_ndims(f_space)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
+    /* Assume entire data space to be printed */
     if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) {
+        hssize_t p_nelmts; /* total selected elmts */
+
         if ((p_nelmts = H5Sget_simple_extent_npoints(f_space)) < 0)
             H5_LIBRARY_ERROR(ENVONLY);
 
         if (NULL ==
-            (sm_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts)))
+            (sm_buf = (unsigned char *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts)))
             H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
 
         /* Read the data */
@@ -2987,6 +2986,10 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
         }
     }
     else {
+        /* Print info */
+        size_t  p_type_nbytes; /* size of memory type */
+        hsize_t p_nelmts;      /* total selected elmts */
+
         switch (binary_order) {
             case 1: {
                 if ((p_type = h5str_get_native_type(f_type)) < 0)
@@ -3017,109 +3020,102 @@ h5str_dump_simple_dset(JNIEnv *env, FILE *stream, hid_t dset, int binary_order)
             }
         }
 
-        if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) {
-            if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
-                H5_LIBRARY_ERROR(ENVONLY);
+        /* Calculate the number of elements we're going to print */
+        p_nelmts = 1;
 
-            /* Calculate the number of elements we're going to print */
-            p_nelmts = 1;
-
-            if (ndims > 0) {
-                for (i = 0; i < (size_t)ndims; i++)
-                    p_nelmts *= total_size[i];
-            } /* end if */
+        if (sndims > 0) {
+            for (i = 0; i < (size_t)sndims; i++)
+                p_nelmts *= total_size[i];
+        } /* end if */
 
-            if (p_nelmts > 0) {
-                /* Check if we have VL data in the dataset's datatype */
-                if (h5str_detect_vlen(p_type) != 0)
-                    vl_data = 1;
+        if (p_nelmts > 0) {
+            /* Check if we have VL data in the dataset's datatype */
+            if (h5str_detect_vlen(p_type) != 0)
+                vl_data = 1;
 
-                /*
-                 * Determine the strip mine size and allocate a buffer. The strip mine is
-                 * a hyperslab whose size is manageable.
-                 */
-                if (!(sm_nbytes = p_type_nbytes = H5Tget_size(p_type)))
-                    H5_LIBRARY_ERROR(ENVONLY);
+            /*
+             * Determine the strip mine size and allocate a buffer. The strip mine is
+             * a hyperslab whose size is manageable.
+             */
+            if (!(sm_nbytes = p_type_nbytes = H5Tget_size(p_type)))
+                H5_LIBRARY_ERROR(ENVONLY);
 
-                if (ndims > 0) {
-                    for (i = (size_t)ndims; i > 0; --i) {
-                        hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
-                        if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
-                            size = 1;
-                        sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size));
-                        sm_nbytes *= sm_size[i - 1];
-                    }
+            if (sndims > 0) {
+                for (i = (size_t)sndims; i > 0; --i) {
+                    hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
+                    if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
+                        size = 1;
+                    sm_size[i - 1] = (((total_size[i - 1]) < (size)) ? (total_size[i - 1]) : (size));
+                    sm_nbytes *= sm_size[i - 1];
                 }
+            }
 
-                if (sm_nbytes > 0) {
-                    if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)sm_nbytes)))
-                        H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_dset: failed to allocate sm_buf");
+            if (sm_nbytes > 0) {
+                if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)sm_nbytes)))
+                    H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_dset: failed to allocate sm_buf");
 
-                    sm_nelmts = sm_nbytes / p_type_nbytes;
+                sm_nelmts = sm_nbytes / p_type_nbytes;
 
-                    if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0)
-                        H5_LIBRARY_ERROR(ENVONLY);
-
-                    /* The stripmine loop */
-                    HDmemset(hs_offset, 0, sizeof hs_offset);
-                    HDmemset(zero, 0, sizeof zero);
-
-                    for (elmtno = 0; elmtno < (hsize_t)p_nelmts; elmtno += hs_nelmts) {
-                        /* Calculate the hyperslab size */
-                        if (ndims > 0) {
-                            for (i = 0, hs_nelmts = 1; i < (size_t)ndims; i++) {
-                                hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i]))
-                                                  ? (total_size[i] - hs_offset[i])
-                                                  : (sm_size[i]));
-                                hs_nelmts *= hs_size[i];
-                            }
-
-                            if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) <
-                                0)
-                                H5_LIBRARY_ERROR(ENVONLY);
+                if ((sm_space = H5Screate_simple(1, &sm_nelmts, NULL)) < 0)
+                    H5_LIBRARY_ERROR(ENVONLY);
 
-                            if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) <
-                                0)
-                                H5_LIBRARY_ERROR(ENVONLY);
+                /* The stripmine loop */
+                HDmemset(hs_offset, 0, sizeof hs_offset);
+                HDmemset(zero, 0, sizeof zero);
+
+                for (elmtno = 0; elmtno < (hsize_t)p_nelmts; elmtno += hs_nelmts) {
+                    /* Calculate the hyperslab size */
+                    if (sndims > 0) {
+                        for (i = 0, hs_nelmts = 1; i < (size_t)sndims; i++) {
+                            hs_size[i] = (((total_size[i] - hs_offset[i]) < (sm_size[i]))
+                                              ? (total_size[i] - hs_offset[i])
+                                              : (sm_size[i]));
+                            hs_nelmts *= hs_size[i];
                         }
-                        else {
-                            if (H5Sselect_all(f_space) < 0)
-                                H5_LIBRARY_ERROR(ENVONLY);
 
-                            if (H5Sselect_all(sm_space) < 0)
-                                H5_LIBRARY_ERROR(ENVONLY);
+                        if (H5Sselect_hyperslab(f_space, H5S_SELECT_SET, hs_offset, NULL, hs_size, NULL) < 0)
+                            H5_LIBRARY_ERROR(ENVONLY);
 
-                            hs_nelmts = 1;
-                        }
+                        if (H5Sselect_hyperslab(sm_space, H5S_SELECT_SET, zero, NULL, &hs_nelmts, NULL) < 0)
+                            H5_LIBRARY_ERROR(ENVONLY);
+                    }
+                    else {
+                        if (H5Sselect_all(f_space) < 0)
+                            H5_LIBRARY_ERROR(ENVONLY);
 
-                        /* Read the data */
-                        if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0)
+                        if (H5Sselect_all(sm_space) < 0)
                             H5_LIBRARY_ERROR(ENVONLY);
 
-                        if (binary_order == 99) {
-                            if (h5str_dump_simple_data(ENVONLY, stream, dset, p_type, sm_buf, hs_nelmts) < 0)
-                                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                        }
-                        else {
-                            if (h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts) < 0)
-                                CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                        }
+                        hs_nelmts = 1;
+                    }
 
-                        /* Reclaim any VL memory, if necessary */
-                        if (vl_data) {
-                            if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0)
-                                H5_LIBRARY_ERROR(ENVONLY);
-                        }
+                    /* Read the data */
+                    if (H5Dread(dset, p_type, sm_space, f_space, H5P_DEFAULT, sm_buf) < 0)
+                        H5_LIBRARY_ERROR(ENVONLY);
+
+                    if (binary_order == 99) {
+                        if (h5str_dump_simple_data(ENVONLY, stream, dset, p_type, sm_buf, hs_nelmts) < 0)
+                            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+                    }
+                    else {
+                        if (h5str_render_bin_output(stream, dset, p_type, sm_buf, hs_nelmts) < 0)
+                            CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+                    }
 
-                        /* Calculate the next hyperslab offset */
-                        for (i = (size_t)ndims, carry = 1; i > 0 && carry; --i) {
-                            hs_offset[i - 1] += hs_size[i - 1];
+                    /* Reclaim any VL memory, if necessary */
+                    if (vl_data) {
+                        if (H5Treclaim(p_type, sm_space, H5P_DEFAULT, sm_buf) < 0)
+                            H5_LIBRARY_ERROR(ENVONLY);
+                    }
 
-                            if (hs_offset[i - 1] == total_size[i - 1])
-                                hs_offset[i - 1] = 0;
-                            else
-                                carry = 0;
-                        }
+                    /* Calculate the next hyperslab offset */
+                    for (i = (size_t)sndims, carry = 1; i > 0 && carry; --i) {
+                        hs_offset[i - 1] += hs_size[i - 1];
+
+                        if (hs_offset[i - 1] == total_size[i - 1])
+                            hs_offset[i - 1] = 0;
+                        else
+                            carry = 0;
                     }
                 }
             }
@@ -3148,15 +3144,12 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
 {
     hid_t    f_space = H5I_INVALID_HID; /* file data space */
     hsize_t  alloc_size;
-    int      ndims;                    /* rank of dataspace */
-    unsigned i;                        /* counters  */
-    hsize_t  total_size[H5S_MAX_RANK]; /* total size of dataset*/
-    hssize_t p_nelmts;                 /* total selected elmts */
+    int      sndims;                   /* rank of dataspace */
+    unsigned i;                        /* counters */
+    hsize_t  total_size[H5S_MAX_RANK]; /* total size of dataset */
+    int      ret_value = 0;
 
-    void   *sm_buf = NULL;         /* buffer for raw data */
-    hsize_t sm_size[H5S_MAX_RANK]; /* stripmine size */
-
-    int ret_value = 0;
+    unsigned char *sm_buf = NULL; /* buffer for raw data */
 
     /* VL data special information */
     unsigned int vl_data = 0; /* contains VL datatypes */
@@ -3172,18 +3165,20 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
     if (H5I_INVALID_HID == (f_space = H5Aget_space(attr_id)))
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if ((ndims = H5Sget_simple_extent_ndims(f_space)) < 0)
+    if ((sndims = H5Sget_simple_extent_ndims(f_space)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (H5Tequal(f_type, H5T_STD_REF_DSETREG)) {
+        hssize_t p_nelmts; /* total selected elmts */
+
         if ((p_nelmts = H5Sget_simple_extent_npoints(f_space)) < 0)
             H5_LIBRARY_ERROR(ENVONLY);
 
         if (NULL ==
-            (sm_buf = (H5R_ref_t *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts)))
+            (sm_buf = (unsigned char *)HDcalloc(MAX(sizeof(unsigned), sizeof(H5R_ref_t)), (size_t)p_nelmts)))
             H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
 
         /* Read the data */
@@ -3200,6 +3195,8 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
         }
     }
     else {
+        hsize_t p_nelmts; /* total selected elmts */
+
         switch (binary_order) {
             case 1: {
                 if ((p_type = h5str_get_native_type(f_type)) < 0)
@@ -3230,45 +3227,40 @@ h5str_dump_simple_mem(JNIEnv *env, FILE *stream, hid_t attr_id, int binary_order
             }
         }
 
-        if ((size_t)ndims <= (sizeof(sm_size) / sizeof(sm_size[0]))) {
-            if (H5Sget_simple_extent_dims(f_space, total_size, NULL) < 0)
-                H5_LIBRARY_ERROR(ENVONLY);
-            /* Calculate the number of elements we're going to print */
-            p_nelmts = 1;
+        /* Calculate the number of elements we're going to print */
+        p_nelmts = 1;
 
-            if (ndims > 0) {
-                for (i = 0; i < (size_t)ndims; i++)
-                    p_nelmts *= total_size[i];
-            } /* end if */
+        if (sndims > 0) {
+            for (i = 0; i < (size_t)sndims; i++)
+                p_nelmts *= total_size[i];
+        } /* end if */
 
-            if (p_nelmts > 0) {
-                /* Check if we have VL data in the dataset's datatype */
-                if (h5str_detect_vlen(p_type) != 0)
-                    vl_data = 1;
+        if (p_nelmts > 0) {
+            /* Check if we have VL data in the dataset's datatype */
+            if (h5str_detect_vlen(p_type) != 0)
+                vl_data = 1;
 
-                alloc_size = (size_t)p_nelmts * H5Tget_size(p_type);
-                if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)alloc_size)))
-                    H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
+            alloc_size = (size_t)p_nelmts * H5Tget_size(p_type);
+            if (NULL == (sm_buf = (unsigned char *)HDmalloc((size_t)alloc_size)))
+                H5_OUT_OF_MEMORY_ERROR(ENVONLY, "h5str_dump_simple_mem: failed to allocate sm_buf");
 
-                /* Read the data */
-                if (H5Aread(attr_id, p_type, sm_buf) < 0)
-                    H5_LIBRARY_ERROR(ENVONLY);
+            /* Read the data */
+            if (H5Aread(attr_id, p_type, sm_buf) < 0)
+                H5_LIBRARY_ERROR(ENVONLY);
 
-                if (binary_order == 99) {
-                    if (h5str_dump_simple_data(ENVONLY, stream, attr_id, p_type, sm_buf, (size_t)p_nelmts) <
-                        0)
-                        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                }
-                else {
-                    if (h5str_render_bin_output(stream, attr_id, p_type, sm_buf, (size_t)p_nelmts) < 0)
-                        CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
-                }
+            if (binary_order == 99) {
+                if (h5str_dump_simple_data(ENVONLY, stream, attr_id, p_type, sm_buf, (size_t)p_nelmts) < 0)
+                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+            }
+            else {
+                if (h5str_render_bin_output(stream, attr_id, p_type, sm_buf, (size_t)p_nelmts) < 0)
+                    CHECK_JNI_EXCEPTION(ENVONLY, JNI_FALSE);
+            }
 
-                /* Reclaim any VL memory, if necessary */
-                if (vl_data) {
-                    if (H5Treclaim(p_type, f_space, H5P_DEFAULT, sm_buf) < 0)
-                        H5_LIBRARY_ERROR(ENVONLY);
-                }
+            /* Reclaim any VL memory, if necessary */
+            if (vl_data) {
+                if (H5Treclaim(p_type, f_space, H5P_DEFAULT, sm_buf) < 0)
+                    H5_LIBRARY_ERROR(ENVONLY);
             }
         }
     }
diff --git a/java/test/TestH5Fparams.java b/java/test/TestH5Fparams.java
index 6accc3b..3fcfe3b 100644
--- a/java/test/TestH5Fparams.java
+++ b/java/test/TestH5Fparams.java
@@ -77,6 +77,7 @@ public class TestH5Fparams {
         H5.H5Funmount(-1, null);
     }
 
+    @SuppressWarnings("deprecation")
     @Ignore
     public void testH5Fis_hdf5_text()
     {
diff --git a/java/test/TestH5Ocreate.java b/java/test/TestH5Ocreate.java
index 096abcd..eb57938 100644
--- a/java/test/TestH5Ocreate.java
+++ b/java/test/TestH5Ocreate.java
@@ -449,6 +449,7 @@ public class TestH5Ocreate {
             ((idata)((H5O_iter_data)iter_data).iterdata.get(3)).link_name.compareToIgnoreCase("G1/DS2") == 0);
     }
 
+    @SuppressWarnings("deprecation")
     @Test
     public void testH5Ocomment()
     {
@@ -479,6 +480,7 @@ public class TestH5Ocreate {
         assertTrue("H5Oget_comment: ", obj_comment.compareTo("Test Comment") == 0);
     }
 
+    @SuppressWarnings("deprecation")
     @Test
     public void testH5Ocomment_clear()
     {
@@ -525,6 +527,7 @@ public class TestH5Ocreate {
         assertTrue("H5Oget_comment: ", obj_comment == null);
     }
 
+    @SuppressWarnings("deprecation")
     @Test
     public void testH5Ocomment_by_name()
     {
@@ -548,6 +551,7 @@ public class TestH5Ocreate {
         assertTrue("H5Oget_comment_by_name: ", obj_comment.compareTo("Test Comment") == 0);
     }
 
+    @SuppressWarnings("deprecation")
     @Test
     public void testH5Ocomment_by_name_clear()
     {
diff --git a/java/test/TestH5Oparams.java b/java/test/TestH5Oparams.java
index 280e9fd..296babc 100644
--- a/java/test/TestH5Oparams.java
+++ b/java/test/TestH5Oparams.java
@@ -168,6 +168,7 @@ public class TestH5Oparams {
         H5.H5Ovisit_by_name(-1, "Bogus", -1, -1, null, null, 0, -1);
     }
 
+    @SuppressWarnings("deprecation")
     @Test(expected = HDF5LibraryException.class)
     public void testH5Oset_comment_invalid() throws Throwable
     {
@@ -180,12 +181,14 @@ public class TestH5Oparams {
         H5.H5Oget_comment(-1);
     }
 
+    @SuppressWarnings("deprecation")
     @Test(expected = HDF5LibraryException.class)
     public void testH5Oset_comment_by_name_invalid() throws Throwable
     {
         H5.H5Oset_comment_by_name(-1, "Bogus", null, -1);
     }
 
+    @SuppressWarnings("deprecation")
     @Test(expected = NullPointerException.class)
     public void testH5Oset_comment_by_name_null() throws Throwable
     {