Merge pull request #762 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:h5r_cleanup to develop

* commit 'd0e32b545c41dcc36a69ab146b54b55e7ac9dc07':
  Split internal H5R functionality into H5Rint.c.

14 files changed, 951 insertions, 854 deletions

diff --git a/MANIFEST b/MANIFEST
index 230bf1f..cfe720e 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -810,6 +810,7 @@
 ./src/H5PLextern.h
 ./src/H5R.c
 ./src/H5Rdeprec.c
+./src/H5Rint.c
 ./src/H5Rmodule.h
 ./src/H5Rpkg.h
 ./src/H5Rprivate.h
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 4be86a9..7ee423b 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -532,6 +532,7 @@ IDE_GENERATED_PROPERTIES ("H5PL" "${H5PL_HDRS}" "${H5PL_SOURCES}" )
 set (H5R_SOURCES
     ${HDF5_SRC_DIR}/H5R.c
     ${HDF5_SRC_DIR}/H5Rdeprec.c
+    ${HDF5_SRC_DIR}/H5Rint.c
 )
 set (H5R_HDRS
     ${HDF5_SRC_DIR}/H5Rpkg.h
diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h
index 563f8fa..314ee04 100644
--- a/src/H5Oprivate.h
+++ b/src/H5Oprivate.h
@@ -24,6 +24,9 @@
 #ifndef _H5Oprivate_H
 #define _H5Oprivate_H
 
+/* Early typedefs to avoid circular dependencies */
+typedef struct H5O_t H5O_t;
+
 /* Include the public header file for this API */
 #include "H5Opublic.h"          /* Object header functions              */
 
@@ -44,7 +47,6 @@
 /* Forward references of package typedefs */
 typedef struct H5O_msg_class_t H5O_msg_class_t;
 typedef struct H5O_mesg_t H5O_mesg_t;
-typedef struct H5O_t H5O_t;
 
 /* Values used to create the shared message & attribute heaps */
 /* (Note that these parameters have been tuned so that the resulting heap ID
diff --git a/src/H5R.c b/src/H5R.c
index b000183..8b42b35 100644
--- a/src/H5R.c
+++ b/src/H5R.c
@@ -21,16 +21,13 @@
 /***********/
 /* Headers */
 /***********/
-#include "H5private.h"		/* Generic Functions			*/
-#include "H5ACprivate.h"        /* Metadata cache                       */
-#include "H5Dprivate.h"		/* Datasets				*/
-#include "H5Eprivate.h"		/* Error handling		  	*/
-#include "H5Gprivate.h"		/* Groups				*/
-#include "H5HGprivate.h"	/* Global Heaps				*/
-#include "H5Iprivate.h"		/* IDs			  		*/
-#include "H5MMprivate.h"	/* Memory management			*/
-#include "H5Rpkg.h"		/* References				*/
-#include "H5Sprivate.h"		/* Dataspaces 				*/
+#include "H5private.h"          /* Generic Functions                        */
+#include "H5ACprivate.h"        /* Metadata cache                           */
+#include "H5Eprivate.h"         /* Error handling                           */
+#include "H5Gprivate.h"         /* Groups                                   */
+#include "H5Iprivate.h"         /* IDs                                      */
+#include "H5Rpkg.h"             /* References                               */
+#include "H5Sprivate.h"         /* Dataspaces                               */
 
 
 /****************/
@@ -47,20 +44,11 @@
 /* Local Prototypes */
 /********************/
 
-static herr_t H5R_create(void *ref, H5G_loc_t *loc, const char *name,
-        H5R_type_t ref_type, H5S_t *space, hid_t dxpl_id);
-static H5S_t * H5R_get_region(H5F_t *file, hid_t dxpl_id, const void *_ref);
-static ssize_t H5R_get_name(H5F_t *file, hid_t lapl_id, hid_t dxpl_id, hid_t id,
-    H5R_type_t ref_type, const void *_ref, char *name, size_t size);
-
 
 /*********************/
 /* Package Variables */
 /*********************/
 
-/* Package initialization variable */
-hbool_t H5_PKG_INIT_VAR = FALSE;
-
 
 /*****************************/
 /* Library Private Variables */
@@ -71,274 +59,6 @@ hbool_t H5_PKG_INIT_VAR = FALSE;
 /* Local Variables */
 /*******************/
 
-/* Reference ID class */
-static const H5I_class_t H5I_REFERENCE_CLS[1] = {{
-    H5I_REFERENCE,		/* ID class value */
-    0,				/* Class flags */
-    0,				/* # of reserved IDs for class */
-    NULL			/* Callback routine for closing objects of this class */
-}};
-
-/* Flag indicating "top" of interface has been initialized */
-static hbool_t H5R_top_package_initialize_s = FALSE;
-
-
-
-/*--------------------------------------------------------------------------
-NAME
-   H5R__init_package -- Initialize interface-specific information
-USAGE
-    herr_t H5R__init_package()
-
-RETURNS
-    Non-negative on success/Negative on failure
-DESCRIPTION
-    Initializes any interface-specific data or routines.
-
---------------------------------------------------------------------------*/
-herr_t
-H5R__init_package(void)
-{
-    herr_t ret_value = SUCCEED;         /* Return value */
-
-    FUNC_ENTER_NOAPI_NOINIT
-
-    /* Initialize the atom group for the file IDs */
-    if(H5I_register_type(H5I_REFERENCE_CLS) < 0)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable to initialize interface")
-
-    /* Mark "top" of interface as initialized, too */
-    H5R_top_package_initialize_s = TRUE;
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5R__init_package() */
-
-
-/*--------------------------------------------------------------------------
- NAME
-    H5R_top_term_package
- PURPOSE
-    Terminate various H5R objects
- USAGE
-    void H5R_top_term_package()
- RETURNS
-    void
- DESCRIPTION
-    Release IDs for the atom group, deferring full interface shutdown
-    until later (in H5R_term_package).
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
-     Can't report errors...
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-int
-H5R_top_term_package(void)
-{
-    int	n = 0;
-
-    FUNC_ENTER_NOAPI_NOINIT_NOERR
-
-    if(H5R_top_package_initialize_s) {
-        if(H5I_nmembers(H5I_REFERENCE) > 0) {
-            (void)H5I_clear_type(H5I_REFERENCE, FALSE, FALSE);
-            n++; /*H5I*/
-	    } /* end if */
-
-        /* Mark closed */
-        if(0 == n)
-            H5R_top_package_initialize_s = FALSE;
-    } /* end if */
-
-    FUNC_LEAVE_NOAPI(n)
-} /* end H5R_top_term_package() */
-
-
-/*--------------------------------------------------------------------------
- NAME
-    H5R_term_package
- PURPOSE
-    Terminate various H5R objects
- USAGE
-    void H5R_term_package()
- RETURNS
-    void
- DESCRIPTION
-    Release the atom group and any other resources allocated.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
-     Can't report errors...
-
-     Finishes shutting down the interface, after H5R_top_term_package()
-     is called
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-int
-H5R_term_package(void)
-{
-    int	n = 0;
-
-    FUNC_ENTER_NOAPI_NOINIT_NOERR
-
-    if(H5_PKG_INIT_VAR) {
-        /* Sanity checks */
-        HDassert(0 == H5I_nmembers(H5I_REFERENCE));
-        HDassert(FALSE == H5R_top_package_initialize_s);
-
-        /* Destroy the reference id group */
-        n += (H5I_dec_type_ref(H5I_REFERENCE) > 0);
-
-        /* Mark closed */
-        if(0 == n)
-            H5_PKG_INIT_VAR = FALSE;
-    } /* end if */
-
-    FUNC_LEAVE_NOAPI(n)
-} /* end H5R_term_package() */
-
-
-/*--------------------------------------------------------------------------
- NAME
-    H5R_create
- PURPOSE
-    Creates a particular kind of reference for the user
- USAGE
-    herr_t H5R_create(ref, loc, name, ref_type, space)
-        void *ref;          OUT: Reference created
-        H5G_loc_t *loc;     IN: File location used to locate object pointed to
-        const char *name;   IN: Name of object at location LOC_ID of object
-                                    pointed to
-        H5R_type_t ref_type;    IN: Type of reference to create
-        H5S_t *space;       IN: Dataspace ID with selection, used for Dataset
-                                    Region references.
-
- RETURNS
-    Non-negative on success/Negative on failure
- DESCRIPTION
-    Creates a particular type of reference specified with REF_TYPE, in the
-    space pointed to by REF.  The LOC_ID and NAME are used to locate the object
-    pointed to and the SPACE_ID is used to choose the region pointed to (for
-    Dataset Region references).
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-static herr_t
-H5R_create(void *_ref, H5G_loc_t *loc, const char *name, H5R_type_t ref_type, H5S_t *space, hid_t dxpl_id)
-{
-    H5G_loc_t	obj_loc;		/* Group hier. location of object */
-    H5G_name_t  path;            	/* Object group hier. path */
-    H5O_loc_t   oloc;            	/* Object object location */
-    hbool_t     obj_found = FALSE;      /* Object location found */
-    herr_t ret_value = SUCCEED;         /* Return value */
-
-    FUNC_ENTER_NOAPI_NOINIT
-
-    HDassert(_ref);
-    HDassert(loc);
-    HDassert(name);
-    HDassert(ref_type > H5R_BADTYPE && ref_type < H5R_MAXTYPE);
-
-    /* Set up object location to fill in */
-    obj_loc.oloc = &oloc;
-    obj_loc.path = &path;
-    H5G_loc_reset(&obj_loc);
-
-    /* Find the object */
-    if(H5G_loc_find(loc, name, &obj_loc, H5P_DEFAULT, dxpl_id) < 0)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_NOTFOUND, FAIL, "object not found")
-    obj_found = TRUE;
-
-    switch(ref_type) {
-        case H5R_OBJECT:
-        {
-            hobj_ref_t *ref = (hobj_ref_t *)_ref; /* Get pointer to correct type of reference struct */
-
-            *ref = obj_loc.oloc->addr;
-            break;
-        }
-
-        case H5R_DATASET_REGION:
-        {
-            H5HG_t hobjid;      /* Heap object ID */
-            hdset_reg_ref_t *ref = (hdset_reg_ref_t *)_ref; /* Get pointer to correct type of reference struct */
-            hssize_t buf_size;  /* Size of buffer needed to serialize selection */
-            uint8_t *p;       /* Pointer to OID to store */
-            uint8_t *buf;     /* Buffer to store serialized selection in */
-            unsigned heapid_found;  /* Flag for non-zero heap ID found */
-            unsigned u;        /* local index */
-
-            /* Set up information for dataset region */
-
-            /* Return any previous heap block to the free list if we are garbage collecting */
-            if(H5F_GC_REF(loc->oloc->file)) {
-                /* Check for an existing heap ID in the reference */
-                for(u = 0, heapid_found = 0, p = (uint8_t *)ref; u < H5R_DSET_REG_REF_BUF_SIZE; u++)
-                    if(p[u] != 0) {
-                        heapid_found = 1;
-                        break;
-                    } /* end if */
-
-                if(heapid_found != 0) {
-/* Return heap block to free list */
-                } /* end if */
-            } /* end if */
-
-            /* Zero the heap ID out, may leak heap space if user is re-using reference and doesn't have garbage collection on */
-            HDmemset(ref, 0, H5R_DSET_REG_REF_BUF_SIZE);
-
-            /* Get the amount of space required to serialize the selection */
-            if((buf_size = H5S_SELECT_SERIAL_SIZE(space)) < 0)
-                HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "Invalid amount of space for serializing selection")
-
-            /* Increase buffer size to allow for the dataset OID */
-            buf_size += (hssize_t)sizeof(haddr_t);
-
-            /* Allocate the space to store the serialized information */
-            H5_CHECK_OVERFLOW(buf_size, hssize_t, size_t);
-            if(NULL == (buf = (uint8_t *)H5MM_malloc((size_t)buf_size)))
-                HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
-
-            /* Serialize information for dataset OID into heap buffer */
-            p = (uint8_t *)buf;
-            H5F_addr_encode(loc->oloc->file, &p, obj_loc.oloc->addr);
-
-            /* Serialize the selection into heap buffer */
-            if(H5S_SELECT_SERIALIZE(space, &p) < 0)
-                HGOTO_ERROR(H5E_REFERENCE, H5E_CANTCOPY, FAIL, "Unable to serialize selection")
-
-            /* Save the serialized buffer for later */
-            H5_CHECK_OVERFLOW(buf_size, hssize_t, size_t);
-            if(H5HG_insert(loc->oloc->file, dxpl_id, (size_t)buf_size, buf, &hobjid) < 0)
-                HGOTO_ERROR(H5E_REFERENCE, H5E_WRITEERROR, FAIL, "Unable to serialize selection")
-
-            /* Serialize the heap ID and index for storage in the file */
-            p = (uint8_t *)ref;
-            H5F_addr_encode(loc->oloc->file, &p, hobjid.addr);
-            UINT32ENCODE(p, hobjid.idx);
-
-            /* Free the buffer we serialized data in */
-            H5MM_xfree(buf);
-            break;
-        }
-
-        case H5R_BADTYPE:
-        case H5R_MAXTYPE:
-        default:
-            HDassert("unknown reference type" && 0);
-            HGOTO_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL, "internal error (unknown reference type)")
-    } /* end switch */
-
-done:
-    if(obj_found)
-        H5G_loc_free(&obj_loc);
-
-    FUNC_LEAVE_NOAPI(ret_value)
-}   /* end H5R_create() */
-
 
 /*--------------------------------------------------------------------------
  NAME
@@ -378,23 +98,23 @@ H5Rcreate(void *ref, hid_t loc_id, const char *name, H5R_type_t ref_type, hid_t
     H5TRACE5("e", "*xi*sRti", ref, loc_id, name, ref_type, space_id);
 
     /* Check args */
-    if(ref == NULL)
+    if (ref == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer")
-    if(H5G_loc(loc_id, &loc) < 0)
+    if (H5G_loc(loc_id, &loc) < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
-    if(!name || !*name)
+    if (!name || !*name)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "no name given")
-    if(ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
+    if (ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
-    if(ref_type != H5R_OBJECT && ref_type != H5R_DATASET_REGION)
+    if (ref_type != H5R_OBJECT && ref_type != H5R_DATASET_REGION)
         HGOTO_ERROR(H5E_ARGS, H5E_UNSUPPORTED, FAIL, "reference type not supported")
-    if(space_id == (-1) && ref_type == H5R_DATASET_REGION)
+    if (space_id == (-1) && ref_type == H5R_DATASET_REGION)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "reference region dataspace id must be valid")
-    if(space_id != (-1) && (NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))))
+    if (space_id != (-1) && (NULL == (space = (H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE))))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
 
     /* Create reference */
-    if((ret_value = H5R_create(ref, &loc, name, ref_type, space, H5AC_ind_read_dxpl_id)) < 0)
+    if ((ret_value = H5R_create(ref, &loc, name, ref_type, space, H5AC_ind_read_dxpl_id)) < 0)
         HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable to create reference")
 
 done:
@@ -404,166 +124,6 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
-    H5R_dereference
- PURPOSE
-    Opens the HDF5 object referenced.
- USAGE
-    hid_t H5R_dereference(ref)
-        H5F_t *file;        IN: File the object being dereferenced is within
-        H5R_type_t ref_type;    IN: Type of reference
-        void *ref;          IN: Reference to open.
-
- RETURNS
-    Valid ID on success, Negative on failure
- DESCRIPTION
-    Given a reference to some object, open that object and return an ID for
-    that object.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
-    Currently only set up to work with references to datasets
- EXAMPLES
- REVISION LOG
-    Raymond Lu
-    13 July 2011
-    I added the OAPL_ID parameter for the object being referenced.  It only
-    supports dataset access property list currently.
-
-    M. Scot Breitenfeld
-    3 March 2015
-    Added a check for undefined reference pointer.
---------------------------------------------------------------------------*/
-hid_t
-H5R_dereference(H5F_t *file, hid_t oapl_id, hid_t dxpl_id, H5R_type_t ref_type, const void *_ref, hbool_t app_ref)
-{
-    H5O_loc_t oloc;             /* Object location */
-    H5G_name_t path;            /* Path of object */
-    H5G_loc_t loc;              /* Group location */
-    unsigned rc;		/* Reference count of object */
-    H5O_type_t obj_type;        /* Type of object */
-    hid_t ret_value = H5I_INVALID_HID;  /* Return value */
-
-    FUNC_ENTER_NOAPI_NOINIT
-
-    HDassert(_ref);
-    HDassert(ref_type > H5R_BADTYPE && ref_type < H5R_MAXTYPE);
-    HDassert(file);
-
-    /* Initialize the object location */
-    H5O_loc_reset(&oloc);
-    oloc.file = file;
-
-    switch(ref_type) {
-        case H5R_OBJECT:
-            oloc.addr = *(const hobj_ref_t *)_ref; /* Only object references currently supported */
-	    if(!H5F_addr_defined(oloc.addr) || oloc.addr == 0)
-	      HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Undefined reference pointer")
-	      break;
-            
-        case H5R_DATASET_REGION:
-        {
-            H5HG_t hobjid;  /* Heap object ID */
-            uint8_t *buf;   /* Buffer to store serialized selection in */
-            const uint8_t *p;           /* Pointer to OID to store */
-
-            /* Get the heap ID for the dataset region */
-            p = (const uint8_t *)_ref;
-            H5F_addr_decode(oloc.file, &p, &(hobjid.addr));
-            UINT32DECODE(p, hobjid.idx);
-
-            if(!H5F_addr_defined(hobjid.addr) || hobjid.addr == 0)
-	      HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Undefined reference pointer")
-
-            /* Get the dataset region from the heap (allocate inside routine) */
-            if(NULL == (buf = (uint8_t *)H5HG_read(oloc.file, dxpl_id, &hobjid, NULL, NULL)))
-                HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
-
-            /* Get the object oid for the dataset */
-            p = buf;
-            H5F_addr_decode(oloc.file, &p, &(oloc.addr));
-
-            /* Free the buffer allocated in H5HG_read() */
-            H5MM_xfree(buf);
-        } /* end case */
-        break;
-
-        case H5R_BADTYPE:
-        case H5R_MAXTYPE:
-        default:
-            HDassert("unknown reference type" && 0);
-            HGOTO_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL, "internal error (unknown reference type)")
-    } /* end switch */
-
-    /* Get the # of links for object, and its type */
-    /* (To check to make certain that this object hasn't been deleted since the reference was created) */
-    if(H5O_get_rc_and_type(&oloc, dxpl_id, &rc, &obj_type) < 0 || 0 == rc)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_LINKCOUNT, FAIL, "dereferencing deleted object")
-
-    /* Construct a group location for opening the object */
-    H5G_name_reset(&path);
-    loc.oloc = &oloc;
-    loc.path = &path;
-
-    /* Open the object */
-    switch(obj_type) {
-        case H5O_TYPE_GROUP:
-            {
-                H5G_t *group;               /* Pointer to group to open */
-
-                if(NULL == (group = H5G_open(&loc, dxpl_id)))
-                    HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, FAIL, "not found")
-
-                /* Create an atom for the group */
-                if((ret_value = H5I_register(H5I_GROUP, group, app_ref)) < 0) {
-                    H5G_close(group);
-                    HGOTO_ERROR(H5E_SYM, H5E_CANTREGISTER, FAIL, "can't register group")
-                } /* end if */
-            } /* end case */
-            break;
-
-        case H5O_TYPE_NAMED_DATATYPE:
-            {
-                H5T_t *type;                /* Pointer to datatype to open */
-
-                if(NULL == (type = H5T_open(&loc, dxpl_id)))
-                    HGOTO_ERROR(H5E_DATATYPE, H5E_NOTFOUND, FAIL, "not found")
-
-                /* Create an atom for the datatype */
-                if((ret_value = H5I_register(H5I_DATATYPE, type, app_ref)) < 0) {
-                    H5T_close(type);
-                    HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "can't register datatype")
-                } /* end if */
-            } /* end case */
-            break;
-
-        case H5O_TYPE_DATASET:
-            {
-                H5D_t *dset;                /* Pointer to dataset to open */
-
-                /* Open the dataset */
-                if(NULL == (dset = H5D_open(&loc, oapl_id, dxpl_id)))
-                    HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found")
-
-                /* Create an atom for the dataset */
-                if((ret_value = H5I_register(H5I_DATASET, dset, app_ref)) < 0) {
-                    H5D_close(dset);
-                    HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset")
-                } /* end if */
-            } /* end case */
-            break;
-
-        case H5O_TYPE_UNKNOWN:
-        case H5O_TYPE_NTYPES:
-        default:
-            HGOTO_ERROR(H5E_REFERENCE, H5E_BADTYPE, FAIL, "can't identify type of object referenced")
-     } /* end switch */
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-}   /* end H5R_dereference() */
-
-
-/*--------------------------------------------------------------------------
- NAME
     H5Rdereference2
  PURPOSE
     Opens the HDF5 object referenced.
@@ -601,24 +161,24 @@ H5Rdereference2(hid_t obj_id, hid_t oapl_id, H5R_type_t ref_type, const void *_r
     H5TRACE4("i", "iiRt*x", obj_id, oapl_id, ref_type, _ref);
 
     /* Check args */
-    if(H5G_loc(obj_id, &loc) < 0)
+    if (H5G_loc(obj_id, &loc) < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
-    if(oapl_id < 0)
+    if (oapl_id < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a property list")
-    if(ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
+    if (ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
-    if(_ref == NULL)
+    if (_ref == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer")
 
     /* Verify access property list and get correct dxpl */
-    if(H5P_verify_apl_and_dxpl(&oapl_id, H5P_CLS_DACC, &dxpl_id, obj_id, FALSE) < 0)
+    if (H5P_verify_apl_and_dxpl(&oapl_id, H5P_CLS_DACC, &dxpl_id, obj_id, FALSE) < 0)
         HGOTO_ERROR(H5E_REFERENCE, H5E_CANTSET, FAIL, "can't set access and transfer property lists")
 
     /* Get the file pointer from the entry */
     file = loc.oloc->file;
 
     /* Create reference */
-    if((ret_value = H5R_dereference(file, oapl_id, dxpl_id, ref_type, _ref, TRUE)) < 0)
+    if ((ret_value = H5R_dereference(file, oapl_id, dxpl_id, ref_type, _ref, TRUE)) < 0)
         HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable to dereference object")
 
 done:
@@ -628,75 +188,6 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
-    H5R_get_region
- PURPOSE
-    Retrieves a dataspace with the region pointed to selected.
- USAGE
-    H5S_t *H5R_get_region(file, ref_type, ref)
-        H5F_t *file;        IN: File the object being dereferenced is within
-        void *ref;          IN: Reference to open.
-
- RETURNS
-    Pointer to the dataspace on success, NULL on failure
- DESCRIPTION
-    Given a reference to some object, creates a copy of the dataset pointed
-    to's dataspace and defines a selection in the copy which is the region
-    pointed to.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-static H5S_t *
-H5R_get_region(H5F_t *file, hid_t dxpl_id, const void *_ref)
-{
-    H5O_loc_t oloc;             /* Object location */
-    const uint8_t *p;           /* Pointer to OID to store */
-    H5HG_t hobjid;              /* Heap object ID */
-    uint8_t *buf = NULL;        /* Buffer to store serialized selection in */
-    H5S_t *ret_value;
-
-    FUNC_ENTER_NOAPI_NOINIT
-
-    HDassert(_ref);
-    HDassert(file);
-
-    /* Initialize the object location */
-    H5O_loc_reset(&oloc);
-    oloc.file = file;
-
-    /* Get the heap ID for the dataset region */
-    p = (const uint8_t *)_ref;
-    H5F_addr_decode(oloc.file, &p, &(hobjid.addr));
-    UINT32DECODE(p, hobjid.idx);
-
-    /* Get the dataset region from the heap (allocate inside routine) */
-    if((buf = (uint8_t *)H5HG_read(oloc.file, dxpl_id, &hobjid, NULL, NULL)) == NULL)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, NULL, "Unable to read dataset region information")
-
-    /* Get the object oid for the dataset */
-    p = buf;
-    H5F_addr_decode(oloc.file, &p, &(oloc.addr));
-
-    /* Open and copy the dataset's dataspace */
-    if((ret_value = H5S_read(&oloc, dxpl_id)) == NULL)
-        HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, NULL, "not found")
-
-    /* Unserialize the selection */
-    if(H5S_SELECT_DESERIALIZE(&ret_value, &p) < 0)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTDECODE, NULL, "can't deserialize selection")
-
-done:
-    /* Free the buffer allocated in H5HG_read() */
-    if(buf)
-        H5MM_xfree(buf);
-
-    FUNC_LEAVE_NOAPI(ret_value)
-}   /* end H5R_get_region() */
-
-
-/*--------------------------------------------------------------------------
- NAME
     H5Rget_region
  PURPOSE
     Retrieves a dataspace with the region pointed to selected.
@@ -729,19 +220,19 @@ H5Rget_region(hid_t id, H5R_type_t ref_type, const void *ref)
     H5TRACE3("i", "iRt*x", id, ref_type, ref);
 
     /* Check args */
-    if(H5G_loc(id, &loc) < 0)
+    if (H5G_loc(id, &loc) < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
-    if(ref_type != H5R_DATASET_REGION)
+    if (ref_type != H5R_DATASET_REGION)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
-    if(ref == NULL)
+    if (ref == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer")
 
     /* Get the dataspace with the correct region selected */
-    if((space = H5R_get_region(loc.oloc->file, H5AC_ind_read_dxpl_id, ref)) == NULL)
+    if ((space = H5R_get_region(loc.oloc->file, H5AC_ind_read_dxpl_id, ref)) == NULL)
         HGOTO_ERROR(H5E_REFERENCE, H5E_CANTCREATE, FAIL, "unable to create dataspace")
 
     /* Atomize */
-    if((ret_value = H5I_register(H5I_DATASPACE, space, TRUE)) < 0)
+    if ((ret_value = H5I_register(H5I_DATASPACE, space, TRUE)) < 0)
         HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to register dataspace atom")
 
 done:
@@ -751,92 +242,6 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
-    H5R_get_obj_type
- PURPOSE
-    Retrieves the type of object that an object reference points to
- USAGE
-    H5O_type_t H5R_get_obj_type(file, ref_type, ref)
-        H5F_t *file;        IN: File the object being dereferenced is within
-        H5R_type_t ref_type;    IN: Type of reference to query
-        void *ref;          IN: Reference to query.
-
- RETURNS
-    Success:	An object type defined in H5Gpublic.h
-    Failure:	H5G_UNKNOWN
- DESCRIPTION
-    Given a reference to some object, this function returns the type of object
-    pointed to.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-herr_t
-H5R_get_obj_type(H5F_t *file, hid_t dxpl_id, H5R_type_t ref_type,
-    const void *_ref, H5O_type_t *obj_type)
-{
-    H5O_loc_t oloc;             /* Object location */
-    unsigned rc;		/* Reference count of object    */
-    herr_t ret_value = SUCCEED; /* Return value */
-
-    FUNC_ENTER_NOAPI_NOINIT
-
-    HDassert(file);
-    HDassert(_ref);
-
-    /* Initialize the symbol table entry */
-    H5O_loc_reset(&oloc);
-    oloc.file = file;
-
-    switch(ref_type) {
-        case H5R_OBJECT:
-            /* Get the object oid */
-            oloc.addr = *(const hobj_ref_t *)_ref; /* Only object references currently supported */
-            break;
-
-        case H5R_DATASET_REGION:
-        {
-            H5HG_t hobjid;      /* Heap object ID */
-            const uint8_t *p;   /* Pointer to reference to decode */
-            uint8_t *buf;       /* Buffer to store serialized selection in */
-
-            /* Get the heap ID for the dataset region */
-            p = (const uint8_t *)_ref;
-            H5F_addr_decode(oloc.file, &p, &(hobjid.addr));
-            UINT32DECODE(p, hobjid.idx);
-
-            /* Get the dataset region from the heap (allocate inside routine) */
-            if((buf = (uint8_t *)H5HG_read(oloc.file, dxpl_id, &hobjid, NULL, NULL)) == NULL)
-                HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
-
-            /* Get the object oid for the dataset */
-            p = buf;
-            H5F_addr_decode(oloc.file, &p, &(oloc.addr));
-
-            /* Free the buffer allocated in H5HG_read() */
-            H5MM_xfree(buf);
-        } /* end case */
-        break;
-
-        case H5R_BADTYPE:
-        case H5R_MAXTYPE:
-        default:
-            HDassert("unknown reference type" && 0);
-            HGOTO_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL, "internal error (unknown reference type)")
-    } /* end switch */
-
-    /* Get the # of links for object, and its type */
-    /* (To check to make certain that this object hasn't been deleted since the reference was created) */
-    if(H5O_get_rc_and_type(&oloc, dxpl_id, &rc, obj_type) < 0 || 0 == rc)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_LINKCOUNT, FAIL, "dereferencing deleted object")
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-}   /* end H5R_get_obj_type() */
-
-
-/*--------------------------------------------------------------------------
- NAME
     H5Rget_obj_type2
  PURPOSE
     Retrieves the type of object that an object reference points to
@@ -869,16 +274,16 @@ H5Rget_obj_type2(hid_t id, H5R_type_t ref_type, const void *ref,
     H5TRACE4("e", "iRt*x*Ot", id, ref_type, ref, obj_type);
 
     /* Check args */
-    if(H5G_loc(id, &loc) < 0)
+    if (H5G_loc(id, &loc) < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
-    if(ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
+    if (ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
-    if(ref == NULL)
+    if (ref == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer")
 
     /* Get the object information */
-    if(H5R_get_obj_type(loc.oloc->file, H5AC_ind_read_dxpl_id, ref_type, ref, obj_type) < 0)
-	HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable to determine object type")
+    if (H5R_get_obj_type(loc.oloc->file, H5AC_ind_read_dxpl_id, ref_type, ref, obj_type) < 0)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable to determine object type")
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -887,106 +292,6 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
-    H5R_get_name
- PURPOSE
-    Internal routine to determine a name for the object referenced
- USAGE
-    ssize_t H5R_get_name(f, dxpl_id, ref_type, ref, name, size)
-        H5F_t *f;       IN: Pointer to the file that the reference is pointing
-                            into
-        hid_t lapl_id;  IN: LAPL to use for operation
-        hid_t dxpl_id;  IN: DXPL to use for operation
-        hid_t id;       IN: Location ID given for reference
-        H5R_type_t ref_type;    IN: Type of reference
-        void *ref;      IN: Reference to query.
-        char *name;     OUT: Buffer to place name of object referenced
-        size_t size;    IN: Size of name buffer
-
- RETURNS
-    Non-negative length of the path on success, Negative on failure
- DESCRIPTION
-    Given a reference to some object, determine a path to the object
-    referenced in the file.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
-    This may not be the only path to that object.
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
-static ssize_t
-H5R_get_name(H5F_t *f, hid_t lapl_id, hid_t dxpl_id, hid_t id, H5R_type_t ref_type,
-    const void *_ref, char *name, size_t size)
-{
-    hid_t file_id = H5I_INVALID_HID;    /* ID for file that the reference is in */
-    H5O_loc_t oloc;             /* Object location describing object for reference */
-    ssize_t ret_value = -1;     /* Return value */
-
-    FUNC_ENTER_NOAPI_NOINIT
-
-    /* Check args */
-    HDassert(f);
-    HDassert(_ref);
-
-    /* Initialize the object location */
-    H5O_loc_reset(&oloc);
-    oloc.file = f;
-
-    /* Get address for reference */
-    switch(ref_type) {
-        case H5R_OBJECT:
-            oloc.addr = *(const hobj_ref_t *)_ref;
-            break;
-
-        case H5R_DATASET_REGION:
-        {
-            H5HG_t hobjid;  /* Heap object ID */
-            uint8_t *buf;   /* Buffer to store serialized selection in */
-            const uint8_t *p;           /* Pointer to OID to store */
-
-            /* Get the heap ID for the dataset region */
-            p = (const uint8_t *)_ref;
-            H5F_addr_decode(oloc.file, &p, &(hobjid.addr));
-            UINT32DECODE(p, hobjid.idx);
-
-            /* Get the dataset region from the heap (allocate inside routine) */
-            if((buf = (uint8_t *)H5HG_read(oloc.file, dxpl_id, &hobjid, NULL, NULL)) == NULL)
-                HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
-
-            /* Get the object oid for the dataset */
-            p = buf;
-            H5F_addr_decode(oloc.file, &p, &(oloc.addr));
-
-            /* Free the buffer allocated in H5HG_read() */
-            H5MM_xfree(buf);
-        } /* end case */
-        break;
-
-        case H5R_BADTYPE:
-        case H5R_MAXTYPE:
-        default:
-            HDassert("unknown reference type" && 0);
-            HGOTO_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL, "internal error (unknown reference type)")
-    } /* end switch */
-
-    /* Retrieve file ID for name search */
-    if((file_id = H5I_get_file_id(id, FALSE)) < 0)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, FAIL, "can't retrieve file ID")
-
-    /* Get name, length, etc. */
-    if((ret_value = H5G_get_name_by_addr(file_id, lapl_id, dxpl_id, &oloc, name, size)) < 0)
-        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, FAIL, "can't determine name")
-
-done:
-    /* Close file ID used for search */
-    if(file_id > 0 && H5I_dec_ref(file_id) < 0)
-        HDONE_ERROR(H5E_REFERENCE, H5E_CANTDEC, FAIL, "can't decrement ref count of temp ID")
-
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5R_get_name() */
-
-
-/*--------------------------------------------------------------------------
- NAME
     H5Rget_name
  PURPOSE
     Determines a name for the object referenced
@@ -1030,18 +335,18 @@ H5Rget_name(hid_t id, H5R_type_t ref_type, const void *_ref, char *name,
     H5TRACE5("Zs", "iRt*x*sz", id, ref_type, _ref, name, size);
 
     /* Check args */
-    if(H5G_loc(id, &loc) < 0)
+    if (H5G_loc(id, &loc) < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
-    if(ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
+    if (ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
-    if(_ref == NULL)
+    if (_ref == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer")
 
     /* Get the file pointer from the entry */
     file = loc.oloc->file;
 
     /* Get name */
-    if((ret_value = H5R_get_name(file, H5P_DEFAULT, H5AC_ind_read_dxpl_id, id, ref_type, _ref, name, size)) < 0)
+    if ((ret_value = H5R_get_name(file, H5P_DEFAULT, H5AC_ind_read_dxpl_id, id, ref_type, _ref, name, size)) < 0)
         HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable to determine object path")
 
 done:
diff --git a/src/H5Rdeprec.c b/src/H5Rdeprec.c
index 109bbb4..699f8df 100644
--- a/src/H5Rdeprec.c
+++ b/src/H5Rdeprec.c
@@ -13,11 +13,9 @@
 
 /*-------------------------------------------------------------------------
  *
- * Created:	H5Rdeprec.c
- *		September 13 2007
- *		Quincey Koziol <koziol@hdfgroup.org>
+ * Created:     H5Rdeprec.c
  *
- * Purpose:	Deprecated functions from the H5R interface.  These
+ * Purpose:     Deprecated functions from the H5R interface.  These
  *              functions are here for compatibility purposes and may be
  *              removed in the future.  Applications should switch to the
  *              newer APIs.
@@ -35,13 +33,16 @@
 /***********/
 /* Headers */
 /***********/
-#include "H5private.h"		/* Generic Functions			*/
-#include "H5ACprivate.h"	/* Metadata cache			*/
-#include "H5Eprivate.h"		/* Error handling		  	*/
-#include "H5Gprivate.h"		/* Groups				*/
-#include "H5Oprivate.h"		/* Object headers		  	*/
-#include "H5Rpkg.h"		/* References				*/
-#include "H5Ppublic.h"          /* for using H5P_DATASET_ACCESS_DEFAULT */
+/* Public headers needed by this file */
+#include "H5Ppublic.h"          /* Property lists                           */
+
+/* Private headers needed by this file */
+#include "H5private.h"		    /* Generic Functions                        */
+#include "H5ACprivate.h"	    /* Metadata cache                           */
+#include "H5Eprivate.h"		    /* Error handling                           */
+#include "H5Gprivate.h"		    /* Groups                                   */
+#include "H5Oprivate.h"		    /* Object headers                           */
+#include "H5Rpkg.h"             /* References                               */
 
 
 /****************/
@@ -81,29 +82,22 @@
 
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 
-/*--------------------------------------------------------------------------
- NAME
-    H5Rget_obj_type1
- PURPOSE
-    Retrieves the type of object that an object reference points to
- USAGE
-    H5G_obj_t H5Rget_obj_type1(id, ref_type, ref)
-        hid_t id;       IN: Dataset reference object is in or location ID of
-                            object that the dataset is located within.
-        H5R_type_t ref_type;    IN: Type of reference to query
-        void *ref;          IN: Reference to query.
-
- RETURNS
-    Success:	An object type defined in H5Gpublic.h
-    Failure:	H5G_UNKNOWN
- DESCRIPTION
-    Given a reference to some object, this function returns the type of object
-    pointed to.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
+/*-------------------------------------------------------------------------
+ * Function:    H5Rget_obj_type1
+ *
+ * Purpose:     Retrieves the type of the object that an object points to.
+ *
+ * Parameters:
+ *      id          IN: Dataset reference object is in or location ID of
+ *                      object that the dataset is located within
+ *      ref_type    IN: Type of reference to query
+ *      ref         IN: Reference to query
+ *
+ * Return:      Success:	An object type (as defined in H5Gpublic.h)
+ *              Failure:    H5G_UNKNOWN
+ *
+ *-------------------------------------------------------------------------
+ */
 H5G_obj_t
 H5Rget_obj_type1(hid_t id, H5R_type_t ref_type, const void *ref)
 {
@@ -115,16 +109,16 @@ H5Rget_obj_type1(hid_t id, H5R_type_t ref_type, const void *ref)
     H5TRACE3("Go", "iRt*x", id, ref_type, ref);
 
     /* Check args */
-    if(H5G_loc(id, &loc) < 0)
+    if (H5G_loc(id, &loc) < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, H5G_UNKNOWN, "not a location")
-    if(ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
+    if (ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, H5G_UNKNOWN, "invalid reference type")
-    if(ref == NULL)
+    if (ref == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, H5G_UNKNOWN, "invalid reference pointer")
 
     /* Get the object information */
-    if(H5R_get_obj_type(loc.oloc->file, H5AC_ind_read_dxpl_id, ref_type, ref, &obj_type) < 0)
-	HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, H5G_UNKNOWN, "unable to determine object type")
+    if (H5R_get_obj_type(loc.oloc->file, H5AC_ind_read_dxpl_id, ref_type, ref, &obj_type) < 0)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, H5G_UNKNOWN, "unable to determine object type")
 
     /* Set return value */
     ret_value = H5G_map_obj_type(obj_type);
@@ -134,28 +128,22 @@ done:
 }   /* end H5Rget_obj_type1() */
 
 
-/*--------------------------------------------------------------------------
- NAME
-    H5Rdereference1
- PURPOSE
-    Opens the HDF5 object referenced.
- USAGE
-    hid_t H5Rdereference1(ref)
-        hid_t id;       IN: Dataset reference object is in or location ID of
-                            object that the dataset is located within.
-        H5R_type_t ref_type;    IN: Type of reference to create
-        void *ref;      IN: Reference to open.
-
- RETURNS
-    Valid ID on success, Negative on failure
- DESCRIPTION
-    Given a reference to some object, open that object and return an ID for
-    that object.
- GLOBAL VARIABLES
- COMMENTS, BUGS, ASSUMPTIONS
- EXAMPLES
- REVISION LOG
---------------------------------------------------------------------------*/
+/*-------------------------------------------------------------------------
+ * Function:    H5Rdereference1
+ *
+ * Purpose:     Opens the HDF5 object referenced.
+ *
+ * Parameters:
+ *      id          IN: Dataset reference object is in or location ID of
+ *                      object that the dataset is located within
+ *      ref_type    IN: Type of reference to create
+ *      ref         IN: Reference to open
+ *
+ * Return:      Success:	Valid HDF5 ID
+ *              Failure:    Negative
+ *
+ *-------------------------------------------------------------------------
+ */
 hid_t
 H5Rdereference1(hid_t obj_id, H5R_type_t ref_type, const void *_ref)
 {
@@ -167,18 +155,18 @@ H5Rdereference1(hid_t obj_id, H5R_type_t ref_type, const void *_ref)
     H5TRACE3("i", "iRt*x", obj_id, ref_type, _ref);
 
     /* Check args */
-    if(H5G_loc(obj_id, &loc) < 0)
+    if (H5G_loc(obj_id, &loc) < 0)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a location")
-    if(ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
+    if (ref_type <= H5R_BADTYPE || ref_type >= H5R_MAXTYPE)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference type")
-    if(_ref == NULL)
+    if (_ref == NULL)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid reference pointer")
 
     /* Get the file pointer from the entry */
     file = loc.oloc->file;
 
     /* Create reference */
-    if((ret_value = H5R_dereference(file, H5P_DATASET_ACCESS_DEFAULT, H5AC_ind_read_dxpl_id, ref_type, _ref, TRUE)) < 0)
+    if ((ret_value = H5R_dereference(file, H5P_DATASET_ACCESS_DEFAULT, H5AC_ind_read_dxpl_id, ref_type, _ref, TRUE)) < 0)
         HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable dereference object")
 
 done:
diff --git a/src/H5Rint.c b/src/H5Rint.c
new file mode 100644
index 0000000..716a573
--- /dev/null
+++ b/src/H5Rint.c
@@ -0,0 +1,767 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group.                                               *
+ * Copyright by the Board of Trustees of the University of Illinois.         *
+ * All rights reserved.                                                      *
+ *                                                                           *
+ * This file is part of HDF5.  The full HDF5 copyright notice, including     *
+ * terms governing use, modification, and redistribution, is contained in    *
+ * the COPYING file, which can be found at the root of the source code       *
+ * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * If you do not have access to either file, you may request a copy from     *
+ * help@hdfgroup.org.                                                        *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/****************/
+/* Module Setup */
+/****************/
+
+#include "H5Rmodule.h"          /* This source code file is part of the H5R module */
+
+
+/***********/
+/* Headers */
+/***********/
+#include "H5private.h"          /* Generic Functions                        */
+#include "H5ACprivate.h"        /* Metadata cache                           */
+#include "H5Dprivate.h"         /* Datasets                                 */
+#include "H5Eprivate.h"         /* Error handling                           */
+#include "H5Gprivate.h"         /* Groups                                   */
+#include "H5HGprivate.h"        /* Global Heaps                             */
+#include "H5Iprivate.h"         /* IDs                                      */
+#include "H5MMprivate.h"        /* Memory management                        */
+#include "H5Oprivate.h"         /* Object headers                           */
+#include "H5Rpkg.h"             /* References                               */
+#include "H5Sprivate.h"         /* Dataspaces                               */
+#include "H5Tprivate.h"         /* Datatypes                                */
+
+
+/****************/
+/* Local Macros */
+/****************/
+
+/******************/
+/* Local Typedefs */
+/******************/
+
+/********************/
+/* Local Prototypes */
+/********************/
+
+/*********************/
+/* Package Variables */
+/*********************/
+
+/* Package initialization variable */
+hbool_t H5_PKG_INIT_VAR = FALSE;
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
+/*******************/
+/* Local Variables */
+/*******************/
+
+/* Reference ID class
+ *
+ * NOTE: H5I_REFERENCE is not used by the library and has been deprecated
+ *       with a tentative removal version of 1.12.0. (DER, July 2017)
+ */
+static const H5I_class_t H5I_REFERENCE_CLS[1] = {{
+    H5I_REFERENCE,          /* ID class value                                       */
+    0,                      /* Class flags                                          */
+    0,                      /* # of reserved IDs for class                          */
+    NULL                    /* Callback routine for closing objects of this class   */
+}};
+
+/* Flag indicating "top" of interface has been initialized */
+static hbool_t H5R_top_package_initialize_s = FALSE;
+
+
+/*--------------------------------------------------------------------------
+NAME
+   H5R__init_package -- Initialize interface-specific information
+USAGE
+    herr_t H5R__init_package()
+
+RETURNS
+    Non-negative on success/Negative on failure
+DESCRIPTION
+    Initializes any interface-specific data or routines.
+
+--------------------------------------------------------------------------*/
+herr_t
+H5R__init_package(void)
+{
+    herr_t ret_value = SUCCEED;         /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    /* Initialize the atom group for the file IDs */
+    if (H5I_register_type(H5I_REFERENCE_CLS) < 0)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "unable to initialize interface")
+
+    /* Mark "top" of interface as initialized, too */
+    H5R_top_package_initialize_s = TRUE;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5R__init_package() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5R_top_term_package
+ PURPOSE
+    Terminate various H5R objects
+ USAGE
+    void H5R_top_term_package()
+ RETURNS
+    void
+ DESCRIPTION
+    Release IDs for the atom group, deferring full interface shutdown
+    until later (in H5R_term_package).
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+     Can't report errors...
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+int
+H5R_top_term_package(void)
+{
+    int	n = 0;
+
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    if (H5R_top_package_initialize_s) {
+        if (H5I_nmembers(H5I_REFERENCE) > 0) {
+            (void)H5I_clear_type(H5I_REFERENCE, FALSE, FALSE);
+            n++;
+	    }
+
+        /* Mark closed */
+        if (0 == n)
+            H5R_top_package_initialize_s = FALSE;
+    }
+
+    FUNC_LEAVE_NOAPI(n)
+} /* end H5R_top_term_package() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5R_term_package
+ PURPOSE
+    Terminate various H5R objects
+ USAGE
+    void H5R_term_package()
+ RETURNS
+    void
+ DESCRIPTION
+    Release the atom group and any other resources allocated.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+     Can't report errors...
+
+     Finishes shutting down the interface, after H5R_top_term_package()
+     is called
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+int
+H5R_term_package(void)
+{
+    int	n = 0;
+
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    if (H5_PKG_INIT_VAR) {
+        /* Sanity checks */
+        HDassert(0 == H5I_nmembers(H5I_REFERENCE));
+        HDassert(FALSE == H5R_top_package_initialize_s);
+
+        /* Destroy the reference id group */
+        n += (H5I_dec_type_ref(H5I_REFERENCE) > 0);
+
+        /* Mark closed */
+        if (0 == n)
+            H5_PKG_INIT_VAR = FALSE;
+    }
+
+    FUNC_LEAVE_NOAPI(n)
+} /* end H5R_term_package() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5R_create
+ PURPOSE
+    Creates a particular kind of reference for the user
+ USAGE
+    herr_t H5R_create(ref, loc, name, ref_type, space)
+        void *ref;          OUT: Reference created
+        H5G_loc_t *loc;     IN: File location used to locate object pointed to
+        const char *name;   IN: Name of object at location LOC_ID of object
+                                    pointed to
+        H5R_type_t ref_type;    IN: Type of reference to create
+        H5S_t *space;       IN: Dataspace ID with selection, used for Dataset
+                                    Region references.
+
+ RETURNS
+    Non-negative on success/Negative on failure
+ DESCRIPTION
+    Creates a particular type of reference specified with REF_TYPE, in the
+    space pointed to by REF.  The LOC_ID and NAME are used to locate the object
+    pointed to and the SPACE_ID is used to choose the region pointed to (for
+    Dataset Region references).
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5R_create(void *_ref, H5G_loc_t *loc, const char *name, H5R_type_t ref_type, H5S_t *space, hid_t dxpl_id)
+{
+    H5G_loc_t	obj_loc;		/* Group hier. location of object */
+    H5G_name_t  path;            	/* Object group hier. path */
+    H5O_loc_t   oloc;            	/* Object object location */
+    hbool_t     obj_found = FALSE;      /* Object location found */
+    herr_t ret_value = SUCCEED;         /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    HDassert(_ref);
+    HDassert(loc);
+    HDassert(name);
+    HDassert(ref_type > H5R_BADTYPE && ref_type < H5R_MAXTYPE);
+
+    /* Set up object location to fill in */
+    obj_loc.oloc = &oloc;
+    obj_loc.path = &path;
+    H5G_loc_reset(&obj_loc);
+
+    /* Find the object */
+    if (H5G_loc_find(loc, name, &obj_loc, H5P_DEFAULT, dxpl_id) < 0)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_NOTFOUND, FAIL, "object not found")
+    obj_found = TRUE;
+
+    switch (ref_type) {
+        case H5R_OBJECT:
+        {
+            hobj_ref_t *ref = (hobj_ref_t *)_ref; /* Get pointer to correct type of reference struct */
+
+            *ref = obj_loc.oloc->addr;
+            break;
+        }
+
+        case H5R_DATASET_REGION:
+        {
+            H5HG_t hobjid;      /* Heap object ID */
+            hdset_reg_ref_t *ref = (hdset_reg_ref_t *)_ref; /* Get pointer to correct type of reference struct */
+            hssize_t buf_size;  /* Size of buffer needed to serialize selection */
+            uint8_t *p;       /* Pointer to OID to store */
+            uint8_t *buf;     /* Buffer to store serialized selection in */
+            unsigned heapid_found;  /* Flag for non-zero heap ID found */
+            unsigned u;        /* local index */
+
+            /* Set up information for dataset region */
+
+            /* Return any previous heap block to the free list if we are
+             * garbage collecting
+             */
+            if (H5F_GC_REF(loc->oloc->file)) {
+                /* Check for an existing heap ID in the reference */
+                for (u = 0, heapid_found = 0, p = (uint8_t *)ref; u < H5R_DSET_REG_REF_BUF_SIZE; u++)
+                    if (p[u] != 0) {
+                        heapid_found = 1;
+                        break;
+                    }
+
+                if (heapid_found != 0) {
+                    /* Return heap block to free list */
+                }
+            }
+
+            /* Zero the heap ID out, may leak heap space if user is re-using
+             * reference and doesn't have garbage collection turned on
+             */
+            HDmemset(ref, 0, H5R_DSET_REG_REF_BUF_SIZE);
+
+            /* Get the amount of space required to serialize the selection */
+            if ((buf_size = H5S_SELECT_SERIAL_SIZE(space)) < 0)
+                HGOTO_ERROR(H5E_REFERENCE, H5E_CANTINIT, FAIL, "Invalid amount of space for serializing selection")
+
+            /* Increase buffer size to allow for the dataset OID */
+            buf_size += (hssize_t)sizeof(haddr_t);
+
+            /* Allocate the space to store the serialized information */
+            H5_CHECK_OVERFLOW(buf_size, hssize_t, size_t);
+            if (NULL == (buf = (uint8_t *)H5MM_malloc((size_t)buf_size)))
+                HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
+
+            /* Serialize information for dataset OID into heap buffer */
+            p = (uint8_t *)buf;
+            H5F_addr_encode(loc->oloc->file, &p, obj_loc.oloc->addr);
+
+            /* Serialize the selection into heap buffer */
+            if (H5S_SELECT_SERIALIZE(space, &p) < 0)
+                HGOTO_ERROR(H5E_REFERENCE, H5E_CANTCOPY, FAIL, "Unable to serialize selection")
+
+            /* Save the serialized buffer for later */
+            H5_CHECK_OVERFLOW(buf_size, hssize_t, size_t);
+            if (H5HG_insert(loc->oloc->file, dxpl_id, (size_t)buf_size, buf, &hobjid) < 0)
+                HGOTO_ERROR(H5E_REFERENCE, H5E_WRITEERROR, FAIL, "Unable to serialize selection")
+
+            /* Serialize the heap ID and index for storage in the file */
+            p = (uint8_t *)ref;
+            H5F_addr_encode(loc->oloc->file, &p, hobjid.addr);
+            UINT32ENCODE(p, hobjid.idx);
+
+            /* Free the buffer we serialized data in */
+            H5MM_xfree(buf);
+            break;
+        } /* end case H5R_DATASET_REGION */
+
+        case H5R_BADTYPE:
+        case H5R_MAXTYPE:
+        default:
+            HDassert("unknown reference type" && 0);
+            HGOTO_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL, "internal error (unknown reference type)")
+    } /* end switch */
+
+done:
+    if (obj_found)
+        H5G_loc_free(&obj_loc);
+
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5R_create() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5R_dereference
+ PURPOSE
+    Opens the HDF5 object referenced.
+ USAGE
+    hid_t H5R_dereference(ref)
+        H5F_t *file;        IN: File the object being dereferenced is within
+        H5R_type_t ref_type;    IN: Type of reference
+        void *ref;          IN: Reference to open.
+
+ RETURNS
+    Valid ID on success, Negative on failure
+ DESCRIPTION
+    Given a reference to some object, open that object and return an ID for
+    that object.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+    Currently only set up to work with references to datasets
+ EXAMPLES
+ REVISION LOG
+    Raymond Lu
+    13 July 2011
+    I added the OAPL_ID parameter for the object being referenced.  It only
+    supports dataset access property list currently.
+
+    M. Scot Breitenfeld
+    3 March 2015
+    Added a check for undefined reference pointer.
+--------------------------------------------------------------------------*/
+hid_t
+H5R_dereference(H5F_t *file, hid_t oapl_id, hid_t dxpl_id, H5R_type_t ref_type, const void *_ref, hbool_t app_ref)
+{
+    H5O_loc_t oloc;             /* Object location */
+    H5G_name_t path;            /* Path of object */
+    H5G_loc_t loc;              /* Group location */
+    unsigned rc;		/* Reference count of object */
+    H5O_type_t obj_type;        /* Type of object */
+    hid_t ret_value = H5I_INVALID_HID;  /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    HDassert(_ref);
+    HDassert(ref_type > H5R_BADTYPE && ref_type < H5R_MAXTYPE);
+    HDassert(file);
+
+    /* Initialize the object location */
+    H5O_loc_reset(&oloc);
+    oloc.file = file;
+
+    switch (ref_type) {
+        case H5R_OBJECT:
+        {
+            oloc.addr = *(const hobj_ref_t *)_ref; /* Only object references currently supported */
+            if (!H5F_addr_defined(oloc.addr) || oloc.addr == 0)
+                HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Undefined reference pointer")
+            break;
+        }
+
+        case H5R_DATASET_REGION:
+        {
+            H5HG_t hobjid;  /* Heap object ID */
+            uint8_t *buf;   /* Buffer to store serialized selection in */
+            const uint8_t *p;           /* Pointer to OID to store */
+
+            /* Get the heap ID for the dataset region */
+            p = (const uint8_t *)_ref;
+            H5F_addr_decode(oloc.file, &p, &(hobjid.addr));
+            UINT32DECODE(p, hobjid.idx);
+
+            if (!H5F_addr_defined(hobjid.addr) || hobjid.addr == 0)
+                HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Undefined reference pointer")
+
+            /* Get the dataset region from the heap (allocate inside routine) */
+            if (NULL == (buf = (uint8_t *)H5HG_read(oloc.file, dxpl_id, &hobjid, NULL, NULL)))
+                HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
+
+            /* Get the object oid for the dataset */
+            p = buf;
+            H5F_addr_decode(oloc.file, &p, &(oloc.addr));
+
+            /* Free the buffer allocated in H5HG_read() */
+            H5MM_xfree(buf);
+            break;
+        } /* end case H5R_DATASET_REGION */
+
+        case H5R_BADTYPE:
+        case H5R_MAXTYPE:
+        default:
+            HDassert("unknown reference type" && 0);
+            HGOTO_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL, "internal error (unknown reference type)")
+    } /* end switch */
+
+    /* Get the # of links for object, and its type
+     * (To check to make certain that this object hasn't been deleted
+     *  since the reference was created)
+     */
+    if (H5O_get_rc_and_type(&oloc, dxpl_id, &rc, &obj_type) < 0 || 0 == rc)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_LINKCOUNT, FAIL, "dereferencing deleted object")
+
+    /* Construct a group location for opening the object */
+    H5G_name_reset(&path);
+    loc.oloc = &oloc;
+    loc.path = &path;
+
+    /* Open the object */
+    switch (obj_type) {
+        case H5O_TYPE_GROUP:
+        {
+            H5G_t *group;               /* Pointer to group to open */
+
+            if (NULL == (group = H5G_open(&loc, dxpl_id)))
+                HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, FAIL, "not found")
+
+            /* Create an atom for the group */
+            if ((ret_value = H5I_register(H5I_GROUP, group, app_ref)) < 0) {
+                H5G_close(group);
+                HGOTO_ERROR(H5E_SYM, H5E_CANTREGISTER, FAIL, "can't register group")
+            }
+
+            break;
+        }
+
+        case H5O_TYPE_NAMED_DATATYPE:
+        {
+            H5T_t *type;                /* Pointer to datatype to open */
+
+            if (NULL == (type = H5T_open(&loc, dxpl_id)))
+                HGOTO_ERROR(H5E_DATATYPE, H5E_NOTFOUND, FAIL, "not found")
+
+            /* Create an atom for the datatype */
+            if ((ret_value = H5I_register(H5I_DATATYPE, type, app_ref)) < 0) {
+                H5T_close(type);
+                HGOTO_ERROR(H5E_DATATYPE, H5E_CANTREGISTER, FAIL, "can't register datatype")
+            }
+
+            break;
+        }
+
+        case H5O_TYPE_DATASET:
+        {
+            H5D_t *dset;                /* Pointer to dataset to open */
+
+            /* Open the dataset */
+            if (NULL == (dset = H5D_open(&loc, oapl_id, dxpl_id)))
+                HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found")
+
+            /* Create an atom for the dataset */
+            if ((ret_value = H5I_register(H5I_DATASET, dset, app_ref)) < 0) {
+                H5D_close(dset);
+                HGOTO_ERROR(H5E_DATASET, H5E_CANTREGISTER, FAIL, "can't register dataset")
+            }
+
+            break;
+        }
+
+        case H5O_TYPE_UNKNOWN:
+        case H5O_TYPE_NTYPES:
+        default:
+            HGOTO_ERROR(H5E_REFERENCE, H5E_BADTYPE, FAIL, "can't identify type of object referenced")
+     } /* end switch */
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5R_dereference() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5R_get_region
+ PURPOSE
+    Retrieves a dataspace with the region pointed to selected.
+ USAGE
+    H5S_t *H5R_get_region(file, ref_type, ref)
+        H5F_t *file;        IN: File the object being dereferenced is within
+        void *ref;          IN: Reference to open.
+
+ RETURNS
+    Pointer to the dataspace on success, NULL on failure
+ DESCRIPTION
+    Given a reference to some object, creates a copy of the dataset pointed
+    to's dataspace and defines a selection in the copy which is the region
+    pointed to.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+H5S_t *
+H5R_get_region(H5F_t *file, hid_t dxpl_id, const void *_ref)
+{
+    H5O_loc_t oloc;             /* Object location */
+    const uint8_t *p;           /* Pointer to OID to store */
+    H5HG_t hobjid;              /* Heap object ID */
+    uint8_t *buf = NULL;        /* Buffer to store serialized selection in */
+    H5S_t *ret_value;
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    HDassert(_ref);
+    HDassert(file);
+
+    /* Initialize the object location */
+    H5O_loc_reset(&oloc);
+    oloc.file = file;
+
+    /* Get the heap ID for the dataset region */
+    p = (const uint8_t *)_ref;
+    H5F_addr_decode(oloc.file, &p, &(hobjid.addr));
+    UINT32DECODE(p, hobjid.idx);
+
+    /* Get the dataset region from the heap (allocate inside routine) */
+    if ((buf = (uint8_t *)H5HG_read(oloc.file, dxpl_id, &hobjid, NULL, NULL)) == NULL)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, NULL, "Unable to read dataset region information")
+
+    /* Get the object oid for the dataset */
+    p = buf;
+    H5F_addr_decode(oloc.file, &p, &(oloc.addr));
+
+    /* Open and copy the dataset's dataspace */
+    if ((ret_value = H5S_read(&oloc, dxpl_id)) == NULL)
+        HGOTO_ERROR(H5E_DATASPACE, H5E_NOTFOUND, NULL, "not found")
+
+    /* Unserialize the selection */
+    if (H5S_SELECT_DESERIALIZE(&ret_value, &p) < 0)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTDECODE, NULL, "can't deserialize selection")
+
+done:
+    /* Free the buffer allocated in H5HG_read() */
+    if (buf)
+        H5MM_xfree(buf);
+
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5R_get_region() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5R_get_obj_type
+ PURPOSE
+    Retrieves the type of object that an object reference points to
+ USAGE
+    H5O_type_t H5R_get_obj_type(file, ref_type, ref)
+        H5F_t *file;        IN: File the object being dereferenced is within
+        H5R_type_t ref_type;    IN: Type of reference to query
+        void *ref;          IN: Reference to query.
+
+ RETURNS
+    Success:	An object type defined in H5Gpublic.h
+    Failure:	H5G_UNKNOWN
+ DESCRIPTION
+    Given a reference to some object, this function returns the type of object
+    pointed to.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5R_get_obj_type(H5F_t *file, hid_t dxpl_id, H5R_type_t ref_type,
+    const void *_ref, H5O_type_t *obj_type)
+{
+    H5O_loc_t oloc;             /* Object location */
+    unsigned rc;		/* Reference count of object    */
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    HDassert(file);
+    HDassert(_ref);
+
+    /* Initialize the symbol table entry */
+    H5O_loc_reset(&oloc);
+    oloc.file = file;
+
+    switch (ref_type) {
+        case H5R_OBJECT:
+        {
+            /* Get the object oid */
+            oloc.addr = *(const hobj_ref_t *)_ref; /* Only object references currently supported */
+            break;
+        }
+
+        case H5R_DATASET_REGION:
+        {
+            H5HG_t hobjid;      /* Heap object ID */
+            const uint8_t *p;   /* Pointer to reference to decode */
+            uint8_t *buf;       /* Buffer to store serialized selection in */
+
+            /* Get the heap ID for the dataset region */
+            p = (const uint8_t *)_ref;
+            H5F_addr_decode(oloc.file, &p, &(hobjid.addr));
+            UINT32DECODE(p, hobjid.idx);
+
+            /* Get the dataset region from the heap (allocate inside routine) */
+            if ((buf = (uint8_t *)H5HG_read(oloc.file, dxpl_id, &hobjid, NULL, NULL)) == NULL)
+                HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
+
+            /* Get the object oid for the dataset */
+            p = buf;
+            H5F_addr_decode(oloc.file, &p, &(oloc.addr));
+
+            /* Free the buffer allocated in H5HG_read() */
+            H5MM_xfree(buf);
+
+            break;
+        }
+
+        case H5R_BADTYPE:
+        case H5R_MAXTYPE:
+        default:
+            HDassert("unknown reference type" && 0);
+            HGOTO_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL, "internal error (unknown reference type)")
+    } /* end switch */
+
+    /* Get the # of links for object, and its type */
+    /* (To check to make certain that this object hasn't been deleted since the reference was created) */
+    if (H5O_get_rc_and_type(&oloc, dxpl_id, &rc, obj_type) < 0 || 0 == rc)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_LINKCOUNT, FAIL, "dereferencing deleted object")
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+}   /* end H5R_get_obj_type() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5R_get_name
+ PURPOSE
+    Internal routine to determine a name for the object referenced
+ USAGE
+    ssize_t H5R_get_name(f, dxpl_id, ref_type, ref, name, size)
+        H5F_t *f;       IN: Pointer to the file that the reference is pointing
+                            into
+        hid_t lapl_id;  IN: LAPL to use for operation
+        hid_t dxpl_id;  IN: DXPL to use for operation
+        hid_t id;       IN: Location ID given for reference
+        H5R_type_t ref_type;    IN: Type of reference
+        void *ref;      IN: Reference to query.
+        char *name;     OUT: Buffer to place name of object referenced
+        size_t size;    IN: Size of name buffer
+
+ RETURNS
+    Non-negative length of the path on success, Negative on failure
+ DESCRIPTION
+    Given a reference to some object, determine a path to the object
+    referenced in the file.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+    This may not be the only path to that object.
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+ssize_t
+H5R_get_name(H5F_t *f, hid_t lapl_id, hid_t dxpl_id, hid_t id, H5R_type_t ref_type,
+    const void *_ref, char *name, size_t size)
+{
+    hid_t file_id = H5I_INVALID_HID;    /* ID for file that the reference is in */
+    H5O_loc_t oloc;             /* Object location describing object for reference */
+    ssize_t ret_value = -1;     /* Return value */
+
+    FUNC_ENTER_NOAPI_NOINIT
+
+    /* Check args */
+    HDassert(f);
+    HDassert(_ref);
+
+    /* Initialize the object location */
+    H5O_loc_reset(&oloc);
+    oloc.file = f;
+
+    /* Get address for reference */
+    switch (ref_type) {
+        case H5R_OBJECT:
+        {
+            oloc.addr = *(const hobj_ref_t *)_ref;
+            break;
+        }
+
+        case H5R_DATASET_REGION:
+        {
+            H5HG_t hobjid;  /* Heap object ID */
+            uint8_t *buf;   /* Buffer to store serialized selection in */
+            const uint8_t *p;           /* Pointer to OID to store */
+
+            /* Get the heap ID for the dataset region */
+            p = (const uint8_t *)_ref;
+            H5F_addr_decode(oloc.file, &p, &(hobjid.addr));
+            UINT32DECODE(p, hobjid.idx);
+
+            /* Get the dataset region from the heap (allocate inside routine) */
+            if ((buf = (uint8_t *)H5HG_read(oloc.file, dxpl_id, &hobjid, NULL, NULL)) == NULL)
+                HGOTO_ERROR(H5E_REFERENCE, H5E_READERROR, FAIL, "Unable to read dataset region information")
+
+            /* Get the object oid for the dataset */
+            p = buf;
+            H5F_addr_decode(oloc.file, &p, &(oloc.addr));
+
+            /* Free the buffer allocated in H5HG_read() */
+            H5MM_xfree(buf);
+
+            break;
+        }
+
+        case H5R_BADTYPE:
+        case H5R_MAXTYPE:
+        default:
+            HDassert("unknown reference type" && 0);
+            HGOTO_ERROR(H5E_REFERENCE, H5E_UNSUPPORTED, FAIL, "internal error (unknown reference type)")
+    } /* end switch */
+
+    /* Retrieve file ID for name search */
+    if ((file_id = H5I_get_file_id(id, FALSE)) < 0)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, FAIL, "can't retrieve file ID")
+
+    /* Get name, length, etc. */
+    if ((ret_value = H5G_get_name_by_addr(file_id, lapl_id, dxpl_id, &oloc, name, size)) < 0)
+        HGOTO_ERROR(H5E_REFERENCE, H5E_CANTGET, FAIL, "can't determine name")
+
+done:
+    /* Close file ID used for search */
+    if (file_id > 0 && H5I_dec_ref(file_id) < 0)
+        HDONE_ERROR(H5E_REFERENCE, H5E_CANTDEC, FAIL, "can't decrement ref count of temp ID")
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5R_get_name() */
+
diff --git a/src/H5Rmodule.h b/src/H5Rmodule.h
index 2eaf050..678a668 100644
--- a/src/H5Rmodule.h
+++ b/src/H5Rmodule.h
@@ -10,13 +10,9 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-/*
- * Programmer:	Quincey Koziol <koziol@hdfgroup.org>
- *		Saturday, September 12, 2015
- *
- * Purpose:	This file contains declarations which define macros for the
- *		H5R package.  Including this header means that the source file
- *		is part of the H5R package.
+/* Purpose: This file contains declarations which define macros for the
+ *          H5R package.  Including this header means that the source file
+ *          is part of the H5R package.
  */
 #ifndef _H5Rmodule_H
 #define _H5Rmodule_H
@@ -31,4 +27,3 @@
 
 #endif /* _H5Rmodule_H */
 
-
diff --git a/src/H5Rpkg.h b/src/H5Rpkg.h
index 6d5036b..129f944 100644
--- a/src/H5Rpkg.h
+++ b/src/H5Rpkg.h
@@ -11,11 +11,7 @@
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
 
-/*
- * Programmer: Quincey Koziol <koziol@hdfgroup.org>
- *             Thursday, September 13, 2007
- *
- * Purpose:     This file contains declarations which are visible
+/* Purpose:     This file contains declarations which are visible
  *              only within the H5R package. Source files outside the
  *              H5R package should include H5Rprivate.h instead.
  */
@@ -30,7 +26,6 @@
 #include "H5Rprivate.h"
 
 /* Other private headers needed by this file */
-#include "H5Fprivate.h"         /* File access				*/
 
 /**************************/
 /* Package Private Macros */
@@ -51,12 +46,5 @@
 /* Package Private Prototypes */
 /******************************/
 
-/* General functions */
-H5_DLL herr_t H5R_get_obj_type(H5F_t *file, hid_t dxpl_id, H5R_type_t ref_type,
-    const void *_ref, H5O_type_t *obj_type);
-H5_DLL hid_t H5R_dereference(H5F_t *file, hid_t dapl_id, hid_t dxpl_id, H5R_type_t ref_type,
-    const void *_ref, hbool_t app_ref);
-
-
 #endif /* _H5Rpkg_H */
 
diff --git a/src/H5Rprivate.h b/src/H5Rprivate.h
index 7efa225..35e63d2 100644
--- a/src/H5Rprivate.h
+++ b/src/H5Rprivate.h
@@ -20,10 +20,40 @@
 #include "H5Rpublic.h"
 
 /* Private headers needed by this file */
+#include "H5Fprivate.h"         /* Files                                    */
+#include "H5Gprivate.h"         /* Groups                                   */
+#include "H5Oprivate.h"         /* Object headers                           */
+#include "H5Sprivate.h"         /* Dataspaces                               */
 
-/* Internal data structures */
 
-/* Private functions */
+/**************************/
+/* Library Private Macros */
+/**************************/
+
+
+/****************************/
+/* Library Private Typedefs */
+/****************************/
+
+
+/*****************************/
+/* Library Private Variables */
+/*****************************/
+
+
+/******************************/
+/* Library Private Prototypes */
+/******************************/
+
+H5_DLL herr_t H5R_create(void *ref, H5G_loc_t *loc, const char *name,
+    H5R_type_t ref_type, H5S_t *space, hid_t dxpl_id);
+H5_DLL H5S_t * H5R_get_region(H5F_t *file, hid_t dxpl_id, const void *_ref);
+H5_DLL ssize_t H5R_get_name(H5F_t *file, hid_t lapl_id, hid_t dxpl_id, hid_t id,
+    H5R_type_t ref_type, const void *_ref, char *name, size_t size);
+H5_DLL herr_t H5R_get_obj_type(H5F_t *file, hid_t dxpl_id, H5R_type_t ref_type,
+    const void *_ref, H5O_type_t *obj_type);
+H5_DLL hid_t H5R_dereference(H5F_t *file, hid_t dapl_id, hid_t dxpl_id, H5R_type_t ref_type,
+    const void *_ref, hbool_t app_ref);
 
 #endif  /* _H5Rprivate_H */
 
diff --git a/src/H5Rpublic.h b/src/H5Rpublic.h
index 446b7cd..598bafd 100644
--- a/src/H5Rpublic.h
+++ b/src/H5Rpublic.h
@@ -22,40 +22,59 @@
 #include "H5Gpublic.h"
 #include "H5Ipublic.h"
 
-/*
- * Reference types allowed.
- */
-typedef enum {
-    H5R_BADTYPE     =   (-1),   /*invalid Reference Type                     */
-    H5R_OBJECT,                 /*Object reference                           */
-    H5R_DATASET_REGION,         /*Dataset Region Reference                   */
-    H5R_MAXTYPE                 /*highest type (Invalid as true type)	     */
-} H5R_type_t;
+/*****************/
+/* Public Macros */
+/*****************/
 
 /* Note! Be careful with the sizes of the references because they should really
  * depend on the run-time values in the file.  Unfortunately, the arrays need
- * to be defined at compile-time, so we have to go with the worst case sizes for
- * them.  -QAK
+ * to be defined at compile-time, so we have to go with the worst case sizes
+ * for them.  -QAK
+ */
+#define H5R_OBJ_REF_BUF_SIZE        sizeof(haddr_t)
+
+/* 4 is used instead of sizeof(int) to permit portability between the Crays
+ * and other machines (the heap ID is always encoded as an int32 anyway).
+ */
+#define H5R_DSET_REG_REF_BUF_SIZE   (sizeof(haddr_t) + 4)
+
+/*******************/
+/* Public Typedefs */
+/*******************/
+
+/* Reference types */
+typedef enum H5R_type_t {
+    H5R_BADTYPE     =   (-1),   /* Invalid Reference Type               */
+    H5R_OBJECT,                 /* Object reference                     */
+    H5R_DATASET_REGION,         /* Dataset Region Reference             */
+    H5R_MAXTYPE                 /* Highest type (Invalid as true type)  */
+} H5R_type_t;
+
+/* Object reference structure for user's code
+ * This needs to be large enough to store largest haddr_t on a worst case
+ * machine (8 bytes currently).
+ */
+typedef haddr_t hobj_ref_t;
+
+/* Dataset Region reference structure for user's code
+ * (Buffer to store heap ID and index)
+ * This needs to be large enough to store largest haddr_t in a worst case
+ * machine (8 bytes currently) plus an int
  */
-#define H5R_OBJ_REF_BUF_SIZE    sizeof(haddr_t)
-/* Object reference structure for user's code */
-typedef haddr_t hobj_ref_t; /* Needs to be large enough to store largest haddr_t in a worst case machine (ie. 8 bytes currently) */
+typedef unsigned char hdset_reg_ref_t[H5R_DSET_REG_REF_BUF_SIZE];
 
-#define H5R_DSET_REG_REF_BUF_SIZE    (sizeof(haddr_t)+4)
-/* 4 is used instead of sizeof(int) to permit portability between
-   the Crays and other machines (the heap ID is always encoded as an int32 anyway)
-*/
-/* Dataset Region reference structure for user's code */
-typedef unsigned char hdset_reg_ref_t[H5R_DSET_REG_REF_BUF_SIZE];/* Buffer to store heap ID and index */
-/* Needs to be large enough to store largest haddr_t in a worst case machine (ie. 8 bytes currently) plus an int */
+/********************/
+/* Public Variables */
+/********************/
 
-/* Publicly visible data structures */
+/*********************/
+/* Public Prototypes */
+/*********************/
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
-/* Functions in H5R.c */
 H5_DLL herr_t H5Rcreate(void *ref, hid_t loc_id, const char *name,
 			 H5R_type_t ref_type, hid_t space_id);
 H5_DLL hid_t H5Rdereference2(hid_t obj_id, hid_t oapl_id, H5R_type_t ref_type, const void *ref);
@@ -63,7 +82,7 @@ H5_DLL hid_t H5Rget_region(hid_t dataset, H5R_type_t ref_type, const void *ref);
 H5_DLL herr_t H5Rget_obj_type2(hid_t id, H5R_type_t ref_type, const void *_ref,
     H5O_type_t *obj_type);
 H5_DLL ssize_t H5Rget_name(hid_t loc_id, H5R_type_t ref_type, const void *ref,
-    char *name/*out*/, size_t size);
+    char *name /*out*/, size_t size);
 
 /* Symbols defined for compatibility with previous versions of the HDF5 API.
  *
@@ -71,12 +90,6 @@ H5_DLL ssize_t H5Rget_name(hid_t loc_id, H5R_type_t ref_type, const void *ref,
  */
 #ifndef H5_NO_DEPRECATED_SYMBOLS
 
-/* Macros */
-
-
-/* Typedefs */
-
-
 /* Function prototypes */
 H5_DLL H5G_obj_t H5Rget_obj_type1(hid_t id, H5R_type_t ref_type, const void *_ref);
 H5_DLL hid_t H5Rdereference1(hid_t obj_id, H5R_type_t ref_type, const void *ref);
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index 8934726..f125035 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -17,6 +17,9 @@
 #ifndef _H5Sprivate_H
 #define _H5Sprivate_H
 
+/* Early typedefs to avoid circular dependencies */
+typedef struct H5S_t H5S_t;
+
 /* Include package's public header */
 #include "H5Spublic.h"
 
@@ -44,7 +47,6 @@
 #define H5S_GET_SEQ_LIST_SORTED         0x0001
 
 /* Forward references of package typedefs */
-typedef struct H5S_t H5S_t;
 typedef struct H5S_extent_t H5S_extent_t;
 typedef struct H5S_pnt_node_t H5S_pnt_node_t;
 typedef struct H5S_hyper_span_t H5S_hyper_span_t;
diff --git a/src/H5Tprivate.h b/src/H5Tprivate.h
index f2da62e..17cdc49 100644
--- a/src/H5Tprivate.h
+++ b/src/H5Tprivate.h
@@ -17,6 +17,9 @@
 #ifndef _H5Tprivate_H
 #define _H5Tprivate_H
 
+/* Early typedefs to avoid circular dependencies */
+typedef struct H5T_t H5T_t;
+
 /* Get package's public header */
 #include "H5Tpublic.h"
 
@@ -45,7 +48,6 @@
 #endif /* H5T_MODULE */
 
 /* Forward references of package typedefs (declared in H5Tpkg.h) */
-typedef struct H5T_t H5T_t;
 typedef struct H5T_stats_t H5T_stats_t;
 typedef struct H5T_path_t H5T_path_t;
 
diff --git a/src/H5Zprivate.h b/src/H5Zprivate.h
index fe182ad..26e35a7 100644
--- a/src/H5Zprivate.h
+++ b/src/H5Zprivate.h
@@ -18,6 +18,9 @@
 #ifndef _H5Zprivate_H
 #define _H5Zprivate_H
 
+/* Early typedefs to avoid circular dependencies */
+typedef struct H5Z_filter_info_t H5Z_filter_info_t;
+
 /* Include package's public header */
 #include "H5Zpublic.h"
 
@@ -49,7 +52,7 @@
 /****************************/
 
 /* Structure to store information about each filter's parameters */
-typedef struct H5Z_filter_info_t {
+struct H5Z_filter_info_t {
     H5Z_filter_t	id;		/*filter identification number	     */
     unsigned		flags;		/*defn and invocation flags	     */
     char		_name[H5Z_COMMON_NAME_LEN];	/*internal filter name		     */
@@ -57,7 +60,7 @@ typedef struct H5Z_filter_info_t {
     size_t		cd_nelmts;	/*number of elements in cd_values[]  */
     unsigned		_cd_values[H5Z_COMMON_CD_VALUES];	/*internal client data values		     */
     unsigned		*cd_values;	/*client data values		     */
-} H5Z_filter_info_t;
+};
 
 /*****************************/
 /* Library-private Variables */
diff --git a/src/Makefile.am b/src/Makefile.am
index 9a64717..ad29e2a 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -98,7 +98,7 @@ libhdf5_la_SOURCES= H5.c H5checksum.c H5dbg.c H5system.c H5timer.c H5trace.c \
         H5Plapl.c H5Plcpl.c H5Pocpl.c H5Pocpypl.c H5Pstrcpl.c H5Ptest.c \
         H5PB.c \
         H5PL.c H5PLint.c H5PLpath.c H5PLplugin_cache.c \
-        H5R.c H5Rdeprec.c \
+        H5R.c H5Rint.c H5Rdeprec.c \
         H5UC.c \
         H5RS.c \
         H5S.c H5Sall.c H5Sdbg.c H5Shyper.c H5Snone.c H5Spoint.c \