Merging in latest from upstream (HDFFV/hdf5:refs/heads/develop)

* commit '30ca0cdc9a0b1f7fc1521007c65d9baeb69c9a23':
  fix bad function cast warning
  initialization discards const warning
  testpar/t_2Gio.c: Fix a typo that I think was introduced by a         previous warnings PR.  An array element was assigned to         itself---shape[2]Â =Â shape[2];---instead of being assigned to         chunk[2].
  Reduce casts of HDcalloc()/HDmalloc() that -Wc++-compat required.
  Reduce differences between my -Werror branch and `develop`:
  fix unused function warning

5 files changed, 45 insertions, 40 deletions

diff --git a/java/src/jni/h5Constants.c b/java/src/jni/h5Constants.c
index 77a5d18..8fdca35 100644
--- a/java/src/jni/h5Constants.c
+++ b/java/src/jni/h5Constants.c
@@ -26,9 +26,8 @@ extern "C" {
 #include <stdlib.h>
 #include "h5jni.h"
 
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wmissing-prototypes"
-#pragma GCC diagnostic ignored "-Wunused-parameter"
+H5_GCC_DIAG_OFF(missing-prototypes)
+H5_GCC_DIAG_OFF(unused-parameter)
 
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5_1QUARTER_1HADDR_1MAX(JNIEnv *env, jclass cls) { return (hsize_t)HADDR_MAX/4; }
@@ -366,8 +365,7 @@ JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5ES_1STATUS_1CANCELED(JNIEnv *env, jclass cls) { return H5ES_STATUS_CANCELED; }
 
 /* Java does not have unsigned native types */
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wsign-conversion"
+H5_GCC_DIAG_OFF(sign-conversion)
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1CREAT(JNIEnv *env, jclass cls) { return H5F_ACC_CREAT; }
 JNIEXPORT jint JNICALL
@@ -384,7 +382,7 @@ JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1SWMR_1READ(JNIEnv *env, jclass cls) { return H5F_ACC_SWMR_READ; }
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1ACC_1SWMR_1WRITE(JNIEnv *env, jclass cls) { return H5F_ACC_SWMR_WRITE; }
-#pragma GCC diagnostic pop
+H5_GCC_DIAG_ON(sign-conversion)
 
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5F_1CLOSE_1DEFAULT(JNIEnv *env, jclass cls) { return H5F_CLOSE_DEFAULT; }
@@ -1412,7 +1410,8 @@ Java_hdf_hdf5lib_HDF5Constants_H5Z_1SCALEOFFSET_1USER_1NPARMS(JNIEnv *env, jclas
 JNIEXPORT jint JNICALL
 Java_hdf_hdf5lib_HDF5Constants_H5Z_1FILTER_1ALL(JNIEnv *env, jclass cls) { return H5Z_FILTER_ALL; }
 
-#pragma GCC diagnostic pop
+H5_GCC_DIAG_ON(missing-prototypes)
+H5_GCC_DIAG_ON(unused-parameter)
 
 #ifdef __cplusplus
 } /* end extern "C" */
diff --git a/java/src/jni/h5pDCPLImp.c b/java/src/jni/h5pDCPLImp.c
index c43079f..f5bbcb1 100644
--- a/java/src/jni/h5pDCPLImp.c
+++ b/java/src/jni/h5pDCPLImp.c
@@ -1237,7 +1237,7 @@ done:
  */
 JNIEXPORT jstring JNICALL
 Java_hdf_hdf5lib_H5_H5Pget_1virtual_1dsetname
-    (JNIEnv *env, jclass clss, jlong dcpl_id, jlong index)
+    (JNIEnv *env, jclass clss, jlong dcpl_id, jlong idx)
 {
     ssize_t  buf_size;
     char    *dname = NULL;
@@ -1246,13 +1246,13 @@ Java_hdf_hdf5lib_H5_H5Pget_1virtual_1dsetname
     UNUSED(clss);
 
     /* get the length of the filename */
-    if ((buf_size = H5Pget_virtual_dsetname((hid_t)dcpl_id, (size_t)index, NULL, 0)) < 0)
+    if ((buf_size = H5Pget_virtual_dsetname((hid_t)dcpl_id, (size_t) idx, NULL, 0)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (NULL == (dname = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_virtual_dsetname: memory allocation failed");
 
-    if (H5Pget_virtual_dsetname((hid_t)dcpl_id, (size_t)index, dname, (size_t)buf_size + 1) < 0)
+    if (H5Pget_virtual_dsetname((hid_t)dcpl_id, (size_t) idx, dname, (size_t)buf_size + 1) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
     dname[buf_size] = '\0';
 
@@ -1275,7 +1275,7 @@ done:
  */
 JNIEXPORT jstring JNICALL
 Java_hdf_hdf5lib_H5_H5Pget_1virtual_1filename
-    (JNIEnv *env, jclass clss, jlong dcpl_id, jlong index)
+    (JNIEnv *env, jclass clss, jlong dcpl_id, jlong idx)
 {
     ssize_t  buf_size;
     char    *fname = NULL;
@@ -1284,13 +1284,13 @@ Java_hdf_hdf5lib_H5_H5Pget_1virtual_1filename
     UNUSED(clss);
 
     /* get the length of the filename */
-    if ((buf_size = H5Pget_virtual_filename((hid_t)dcpl_id, (size_t)index, NULL, 0)) < 0)
+    if ((buf_size = H5Pget_virtual_filename((hid_t)dcpl_id, (size_t) idx, NULL, 0)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (NULL == (fname = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Pget_virtual_filename: memory allocation failed");
 
-    if (H5Pget_virtual_filename((hid_t)dcpl_id, (size_t)index, fname, (size_t)buf_size + 1) < 0)
+    if (H5Pget_virtual_filename((hid_t)dcpl_id, (size_t) idx, fname, (size_t)buf_size + 1) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
     fname[buf_size] = '\0';
 
@@ -1313,13 +1313,13 @@ done:
  */
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_H5_H5Pget_1virtual_1srcspace
-    (JNIEnv *env, jclass clss, jlong dcpl_id, jlong index)
+    (JNIEnv *env, jclass clss, jlong dcpl_id, jlong idx)
 {
     hid_t space_id = H5I_INVALID_HID;
 
     UNUSED(clss);
 
-    if ((space_id = H5Pget_virtual_srcspace((hid_t)dcpl_id, (size_t)index)) < 0)
+    if ((space_id = H5Pget_virtual_srcspace((hid_t)dcpl_id, (size_t) idx)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
 done:
@@ -1333,13 +1333,13 @@ done:
  */
 JNIEXPORT jlong JNICALL
 Java_hdf_hdf5lib_H5_H5Pget_1virtual_1vspace
-    (JNIEnv *env, jclass clss, jlong dcpl_id, jlong index)
+    (JNIEnv *env, jclass clss, jlong dcpl_id, jlong idx)
 {
     hid_t space_id = H5I_INVALID_HID;
 
     UNUSED(clss);
 
-    if ((space_id = H5Pget_virtual_vspace((hid_t)dcpl_id, (size_t)index)) < 0)
+    if ((space_id = H5Pget_virtual_vspace((hid_t)dcpl_id, (size_t) idx)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
 done:
diff --git a/java/src/jni/h5plImp.c b/java/src/jni/h5plImp.c
index b43b532..ce42842 100644
--- a/java/src/jni/h5plImp.c
+++ b/java/src/jni/h5plImp.c
@@ -129,7 +129,7 @@ done:
  */
 JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5PLreplace
-  (JNIEnv *env, jclass clss, jobjectArray plugin_path, jint index)
+  (JNIEnv *env, jclass clss, jobjectArray plugin_path, jint idx)
 {
     const char *newPath = NULL;
     herr_t      retVal = FAIL;
@@ -139,12 +139,12 @@ Java_hdf_hdf5lib_H5_H5PLreplace
     if (NULL == plugin_path)
         H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5PLreplace: new path is NULL");
 
-    if (index < 0)
+    if (idx < 0)
         H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5PLreplace: index < 0");
 
     PIN_JAVA_STRING(ENVONLY, plugin_path, newPath, NULL, "H5PLreplace: new path not pinned");
 
-    if ((retVal = H5PLreplace(newPath, (unsigned) index)) < 0)
+    if ((retVal = H5PLreplace(newPath, (unsigned) idx)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
 done:
@@ -159,7 +159,7 @@ done:
  */
 JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5PLinsert
-  (JNIEnv *env, jclass clss, jobjectArray plugin_path, jint index)
+  (JNIEnv *env, jclass clss, jobjectArray plugin_path, jint idx)
 {
     const char *newPath = NULL;
     herr_t      retVal = FAIL;
@@ -169,12 +169,12 @@ Java_hdf_hdf5lib_H5_H5PLinsert
     if (NULL == plugin_path)
         H5_NULL_ARGUMENT_ERROR(ENVONLY, "H5PLinsert: new path is NULL");
 
-    if (index < 0)
+    if (idx < 0)
         H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5PLinsert: index < 0");
 
     PIN_JAVA_STRING(ENVONLY, plugin_path, newPath, NULL, "H5PLinsert: new path not pinned");
 
-    if ((retVal = H5PLinsert(newPath, (unsigned) index)) < 0)
+    if ((retVal = H5PLinsert(newPath, (unsigned) idx)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
 done:
@@ -189,14 +189,14 @@ done:
  */
 JNIEXPORT void JNICALL
 Java_hdf_hdf5lib_H5_H5PLremove
-  (JNIEnv *env, jclass clss, jint index)
+  (JNIEnv *env, jclass clss, jint idx)
 {
     UNUSED(clss);
 
-    if (index < 0)
+    if (idx < 0)
         H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5PLremove: index < 0");
 
-    if (H5PLremove((unsigned) index) < 0)
+    if (H5PLremove((unsigned) idx) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
 done:
@@ -210,7 +210,7 @@ done:
  */
 JNIEXPORT jstring JNICALL
 Java_hdf_hdf5lib_H5_H5PLget
-  (JNIEnv *env, jclass clss, jint index)
+  (JNIEnv *env, jclass clss, jint idx)
 {
     jstring  str = NULL;
     ssize_t  buf_size;
@@ -218,17 +218,17 @@ Java_hdf_hdf5lib_H5_H5PLget
 
     UNUSED(clss);
 
-    if (index < 0)
+    if (idx < 0)
         H5_BAD_ARGUMENT_ERROR(ENVONLY, "H5PLget: index < 0");
 
     /* Get the length of the name */
-    if ((buf_size = H5PLget((unsigned) index, NULL, 0)) < 0)
+    if ((buf_size = H5PLget((unsigned) idx, NULL, 0)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
     if (NULL == (aName = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5PLget: failed to allocate plugin name buffer");
 
-    if ((H5PLget((unsigned) index, aName, (size_t)buf_size + 1)) < 0)
+    if ((H5PLget((unsigned) idx, aName, (size_t)buf_size + 1)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
     aName[buf_size] = '\0';
 
diff --git a/java/src/jni/h5rImp.c b/java/src/jni/h5rImp.c
index def27f4..e24fc2a 100644
--- a/java/src/jni/h5rImp.c
+++ b/java/src/jni/h5rImp.c
@@ -50,7 +50,7 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1object
 
     PIN_JAVA_STRING(ENVONLY, name, refName, NULL, "H5Rcreate_object: reference name not pinned");
 
-    if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
+    if (NULL == (refBuf = HDcalloc(1, H5R_REF_BUF_SIZE)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rcreate_object: failed to allocate reference buffer");
 
     if ((status = H5Rcreate_object((hid_t)loc_id, refName, (hid_t)aid, (const H5R_ref_t *)refBuf)) < 0)
@@ -93,7 +93,7 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1region
 
     PIN_JAVA_STRING(ENVONLY, name, refName, NULL, "H5Rcreate_region: reference name not pinned");
 
-    if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
+    if (NULL == (refBuf = HDcalloc(1, H5R_REF_BUF_SIZE)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rcreate_region: failed to allocate reference buffer");
 
     if ((status = H5Rcreate_region((hid_t)loc_id, refName, space_id, (hid_t)aid, (const H5R_ref_t *)refBuf)) < 0)
@@ -140,7 +140,7 @@ Java_hdf_hdf5lib_H5_H5Rcreate_1attr
 
     PIN_JAVA_STRING(ENVONLY, name, refName, NULL, "H5Rcreate_attr: reference name not pinned");
 
-    if (NULL == (refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
+    if (NULL == (refBuf = HDcalloc(1, H5R_REF_BUF_SIZE)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rcreate_attr: failed to allocate reference buffer");
 
     if ((status = H5Rcreate_attr((hid_t)loc_id, refName, attrName, (hid_t)aid, (const H5R_ref_t *)refBuf)) < 0)
@@ -314,7 +314,7 @@ Java_hdf_hdf5lib_H5_H5Rcopy
 
     PIN_BYTE_ARRAY(ENVONLY, src_ref, src_refBuf, &isCopy, "H5Rcopy: src reference buffer not pinned");
 
-    if (NULL == (dst_refBuf = (unsigned char *) HDcalloc((size_t) 1, H5R_REF_BUF_SIZE)))
+    if (NULL == (dst_refBuf = HDcalloc(1, H5R_REF_BUF_SIZE)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rcreate_attr: failed to allocate dst reference buffer");
 
     if ((status = H5Rcopy((const H5R_ref_t *)src_refBuf, (const H5R_ref_t *)dst_refBuf)) < 0)
@@ -504,7 +504,7 @@ Java_hdf_hdf5lib_H5_H5Rget_1file_1name
     if ((buf_size = H5Rget_file_name((const H5R_ref_t *)refBuf, NULL, 0)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
+    if (NULL == (namePtr = HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_file_name: malloc failed");
 
     if ((check_size = H5Rget_file_name((const H5R_ref_t *)refBuf, namePtr, (size_t)buf_size + 1)) < 0)
@@ -550,7 +550,7 @@ Java_hdf_hdf5lib_H5_H5Rget_1obj_1name
     if ((buf_size = H5Rget_obj_name((const H5R_ref_t *)refBuf, (hid_t)rapl_id, NULL, 0)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
+    if (NULL == (namePtr = HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_obj_name: malloc failed");
 
     if ((check_size = H5Rget_obj_name((const H5R_ref_t *)refBuf, (hid_t)rapl_id, namePtr, (size_t)buf_size + 1)) < 0)
@@ -596,7 +596,7 @@ Java_hdf_hdf5lib_H5_H5Rget_1attr_1name
     if ((buf_size = H5Rget_attr_name((const H5R_ref_t *)refBuf, NULL, 0)) < 0)
         H5_LIBRARY_ERROR(ENVONLY);
 
-    if (NULL == (namePtr = (char *) HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
+    if (NULL == (namePtr = HDmalloc(sizeof(char) * (size_t)buf_size + 1)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_attr_name: malloc failed");
 
     if ((check_size = H5Rget_attr_name((const H5R_ref_t *)refBuf, namePtr, (size_t)buf_size + 1)) < 0)
@@ -862,7 +862,7 @@ Java_hdf_hdf5lib_H5_H5Rget_1name
 
     PIN_BYTE_ARRAY(ENVONLY, ref, refBuf, &isCopy, "H5Rget_name: reference buffer not pinned");
 
-    if (NULL == (aName = (char *) HDmalloc(sizeof(char) * (size_t)size + 1)))
+    if (NULL == (aName = HDmalloc(sizeof(char) * (size_t)size + 1)))
         H5_OUT_OF_MEMORY_ERROR(ENVONLY, "H5Rget_name: failed to allocate referenced object name buffer");
 
     if ((ret_val = (jlong)H5Rget_name((hid_t)loc_id, (H5R_type_t)ref_type, refBuf, aName, (size_t)size + 1)) < 0)
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index 55f7571..f45902f 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -28,6 +28,8 @@ extern "C" {
 #include "hdf5.h"
 #include "h5util.h"
 
+#define SKIP_UNUSED_DUMP_ROUTINES
+
 /* size of hyperslab buffer when a dataset is bigger than H5TOOLS_MALLOCSIZE */
 hsize_t H5TOOLS_BUFSIZE = (32 * 1024 * 1024);  /* 32 MB */
 int     H5TOOLS_TEXT_BLOCK = 16;  /* Number of elements on a line in a text export file */
@@ -52,8 +54,10 @@ void        *edata;
 /* Local Prototypes */
 /********************/
 
+#ifndef SKIP_UNUSED_DUMP_ROUTINES
 static int     h5str_dump_region_blocks(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj);
 static int     h5str_dump_region_points(JNIEnv *env, h5str_t *str, hid_t region, hid_t region_obj);
+#endif
 static int     h5str_is_zero(const void *_mem, size_t size);
 static hid_t   h5str_get_native_type(hid_t type);
 static hid_t   h5str_get_little_endian_type(hid_t type);
@@ -708,7 +712,6 @@ h5str_sprintf
     unsigned char *ucptr = (unsigned char *) in_buf;
     static char    fmt_llong[8], fmt_ullong[8];
     H5T_class_t    tclass = H5T_NO_CLASS;
-    H5T_str_t      pad;
     size_t         typeSize = 0;
     H5T_sign_t     nsign = H5T_SGN_ERROR;
     hid_t          mtid = H5I_INVALID_HID;
@@ -814,7 +817,6 @@ h5str_sprintf
             else {
                 tmp_str = cptr;
             }
-            pad = H5Tget_strpad(tid);
 
             /* Check for NULL pointer for string */
             if (!tmp_str) {
@@ -1482,6 +1484,7 @@ done:
     return ret_value;
 } /* end h5str_dump_region_blocks_data */
 
+#ifndef SKIP_UNUSED_DUMP_ROUTINES
 static int
 h5str_dump_region_blocks
     (JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id)
@@ -1569,6 +1572,7 @@ done:
 
     return ret_value;
 } /* end h5str_dump_region_blocks */
+#endif
 
 /*-------------------------------------------------------------------------
  * Purpose: Print the data values from a dataset referenced by region points.
@@ -1701,6 +1705,7 @@ done:
     return ret_value;
 } /* end h5str_dump_region_points_data */
 
+#ifndef SKIP_UNUSED_DUMP_ROUTINES
 static int
 h5str_dump_region_points
     (JNIEnv *env, h5str_t *str, hid_t region, hid_t region_id)
@@ -1776,6 +1781,7 @@ done:
 
     return ret_value;
 } /* end h5str_dump_region_points */
+#endif
 
 static int
 h5str_is_zero