Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_fixbug into develop

7 files changed, 28 insertions, 26 deletions

diff --git a/config/cmake/HDF5_Examples.cmake.in b/config/cmake/HDF5_Examples.cmake.in
index d30f2ab..bac174a 100644
--- a/config/cmake/HDF5_Examples.cmake.in
+++ b/config/cmake/HDF5_Examples.cmake.in
@@ -48,7 +48,11 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCTEST_CONFIGURATION_TYPE:STRING=${
 ##################################################################
 
 if(NOT DEFINED INSTALLDIR)
-  set(INSTALLDIR "C:/Program Files/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
+  if(WIN32)
+    set(INSTALLDIR "C:/Program Files/HDF_Group/@HDF5_PACKAGE_NAME@/@HDF5_PACKAGE_VERSION@")
+  else()
+    set(INSTALLDIR "@CMAKE_INSTALL_PREFIX@")
+  endif()
 endif()
 
 if(NOT DEFINED CTEST_SOURCE_NAME)
@@ -70,7 +74,7 @@ set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDN
 
 #TAR_SOURCE - name of tarfile
 #if(NOT DEFINED TAR_SOURCE)
-#  set(CTEST_USE_TAR_SOURCE "HDF5Examples-1.10.10-Source")
+#  set(CTEST_USE_TAR_SOURCE "HDF5Examples-1.12.4-Source")
 #endif()
 
 ###############################################################################################################
diff --git a/config/cmake/patch.xml b/config/cmake/patch.xml
index 70571c5..1bdff3e 100644
--- a/config/cmake/patch.xml
+++ b/config/cmake/patch.xml
@@ -1,5 +1,5 @@
 <CPackWiXPatch>
-	<CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll">
+    <CPackWiXFragment Id="CM_CP_libraries.bin.hdf5.dll">
         <Environment Id="PATH" 
              Name="PATH" 
              Value="[CM_DP_libraries.bin]" 
@@ -7,5 +7,5 @@
              Part="last" 
              Action="set" 
              System="yes"/>
-	</CPackWiXFragment>
+    </CPackWiXFragment>
 </CPackWiXPatch>
diff --git a/config/cmake_ext_mod/HDFMacros.cmake b/config/cmake_ext_mod/HDFMacros.cmake
index 147ae2f..b3d97ce 100644
--- a/config/cmake_ext_mod/HDFMacros.cmake
+++ b/config/cmake_ext_mod/HDFMacros.cmake
@@ -14,7 +14,7 @@
 macro (SET_HDF_BUILD_TYPE)
   get_property(_isMultiConfig GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
   if(_isMultiConfig)
-    set(HDF_CFG_NAME ${CTEST_CONFIGURATION_TYPE})
+    set(HDF_CFG_NAME \${CTEST_CONFIGURATION_TYPE})
     set(HDF_BUILD_TYPE ${CMAKE_CFG_INTDIR})
     set(HDF_CFG_BUILD_TYPE \${CMAKE_INSTALL_CONFIG_NAME})
   else()
@@ -170,7 +170,7 @@ macro (HDF_IMPORT_SET_LIB_OPTIONS libtarget libname libtype libversion)
   if (${importtype} MATCHES "IMPORT")
     set (importprefix "${CMAKE_STATIC_LIBRARY_PREFIX}")
   endif ()
-  if (${CMAKE_BUILD_TYPE} MATCHES "Debug")
+  if (${HDF_CFG_NAME} MATCHES "Debug")
     set (IMPORT_LIB_NAME ${LIB_DEBUG_NAME})
   else ()
     set (IMPORT_LIB_NAME ${LIB_RELEASE_NAME})
@@ -273,7 +273,7 @@ macro (HDF_README_PROPERTIES target_fortran)
           set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO 2015")
         else ()
           set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO 2017")
-         endif ()
+        endif ()
       else ()
         set (BINARY_PLATFORM "${BINARY_PLATFORM}, using VISUAL STUDIO ${CMAKE_C_COMPILER_VERSION}")
       endif ()
diff --git a/java/src/hdf/hdf5lib/H5.java b/java/src/hdf/hdf5lib/H5.java
index 807c613..19ca83b 100644
--- a/java/src/hdf/hdf5lib/H5.java
+++ b/java/src/hdf/hdf5lib/H5.java
@@ -70,8 +70,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * In general, arguments to the HDF Java API are straightforward translations from the 'C' API described in the HDF
  * Reference Manual.
  *
- * <center>
- * <table border=2 cellpadding=2>
+ * <table border=1>
  * <caption><b>HDF-5 C types to Java types</b> </caption>
  * <tr>
  * <td><b>HDF-5</b></td>
@@ -107,8 +106,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * <td>Special -- see HDFArray</td>
  * </tr>
  * </table>
- * </center>
- * <center> <b>General Rules for Passing Arguments and Results</b> </center>
+ * <b>General Rules for Passing Arguments and Results</b>
  * <p>
  * In general, arguments passed <b>IN</b> to Java are the analogous basic types, as above. The exception is for arrays,
  * which are discussed below.
@@ -143,7 +141,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * <p>
  * All the routines where this convention is used will have specific documentation of the details, given below.
  * <p>
- * <a NAME="ARRAYS"> <b>Arrays</b> </a>
+ * <b>Arrays</b>
  * <p>
  * HDF5 needs to read and write multi-dimensional arrays of any number type (and records). The HDF5 API describes the
  * layout of the source and destination, and the data for the array passed as a block of bytes, for instance,
@@ -176,7 +174,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * and the parameter <i>data</i> can be any multi-dimensional array of numbers, such as float[][], or int[][][], or
  * Double[][].
  * <p>
- * <a NAME="CONSTANTS"> <b>HDF-5 Constants</b></a>
+ * <b>HDF-5 Constants</b>
  * <p>
  * The HDF-5 API defines a set of constants and enumerated values. Most of these values are available to Java programs
  * via the class <a href="./hdf.hdf5lib.HDF5Constants.html"> <b>HDF5Constants</b></a>. For example, the parameters for
@@ -196,7 +194,7 @@ import hdf.hdf5lib.structs.H5O_info_t;
  * The Java application uses both types of constants the same way, the only difference is that the
  * <b><i>HDF5CDataTypes</i></b> may have different values on different platforms.
  * <p>
- * <a NAME="ERRORS"> <b>Error handling and Exceptions</b></a>
+ * <b>Error handling and Exceptions</b>
  * <p>
  * The HDF5 error API (H5E) manages the behavior of the error stack in the HDF-5 library. This API is omitted from the
  * JHI5. Errors are converted into Java exceptions. This is totally different from the C interface, but is very natural
diff --git a/java/src/hdf/overview.html b/java/src/hdf/overview.html
index edb1b76..e3a032b 100644
--- a/java/src/hdf/overview.html
+++ b/java/src/hdf/overview.html
@@ -90,8 +90,7 @@ like this:
 The <i><b>H5</b> </i>class automatically loads the native method implementations
 and the HDF5 library.
 
-<h3>
-<a NAME="DOWNLOAD"></a>To Obtain</h3>
+<h3>To Obtain</h3>
 The JHI5 is included with the <a href="https://portal.hdfgroup.org/display/support/Downloads">HDF5</a> library.
 
 </body>
diff --git a/test/cork.c b/test/cork.c
index dceaf5a..240be77 100644
--- a/test/cork.c
+++ b/test/cork.c
@@ -286,19 +286,19 @@ static unsigned
 verify_obj_dset_cork(hbool_t swmr)
 {
     /* Variable Declarations */
-    hid_t fid = -1;     /* File ID */
+    hid_t fid = -1;             /* File ID */
     hid_t fapl = -1;            /* File access property list */
     hid_t aid = -1;             /* Attribute ID */
     hid_t sid = -1, sid2 = -1;  /* Dataspace IDs */
     hid_t did = -1, did2 = -1;  /* Dataset IDs */
     hid_t oid = -1;             /* Object ID */
-    hid_t dcpl2;            /* Dataset creation property list */
+    hid_t dcpl2;                /* Dataset creation property list */
     int i = 0;                  /* Local index variable */
-    hsize_t dim[1] = {100}; /* Dataset dimension size */
+    hsize_t dim[1] = {100};     /* Dataset dimension size */
     hsize_t chunk_dim[1] = {7}; /* Dataset chunk dimension size */
     H5O_info_t oinfo, oinfo2;   /* Object metadata information */
     char attrname[500];         /* Name of attribute */
-    unsigned flags;     /* File access flags */
+    unsigned flags;             /* File access flags */
 
     if(swmr) {
         TESTING("cork status for dataset objects with attributes (SWMR)");
@@ -341,7 +341,7 @@ verify_obj_dset_cork(hbool_t swmr)
         TEST_ERROR
 
     /* Attach and write to an attribute to the dataset: DSET */
-    if((aid = H5Acreate2(did, ATTR, H5T_NATIVE_UINT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) 
+    if((aid = H5Acreate2(did, ATTR, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0) 
         TEST_ERROR
 
     /* Verify cork status of the dataset: DSET */
@@ -380,11 +380,11 @@ verify_obj_dset_cork(hbool_t swmr)
         TEST_ERROR
 
     /* Attach 8 attributes to the dataset */
-    for(i = 0;i < 8; i++) {
-        sprintf(attrname, "attr %d", i);
-        if((aid = H5Acreate2(did2, attrname, H5T_NATIVE_UINT, sid2, H5P_DEFAULT, H5P_DEFAULT)) < 0)
+    for(i = 0; i < 8; i++) {
+        HDsprintf(attrname, "attr %d", i);
+        if((aid = H5Acreate2(did2, attrname, H5T_NATIVE_INT, sid, H5P_DEFAULT, H5P_DEFAULT)) < 0)
             TEST_ERROR
-        if(H5Awrite(aid, H5T_NATIVE_UINT, &i) < 0)
+        if(H5Awrite(aid, H5T_NATIVE_INT, &i) < 0)
             TEST_ERROR
         if(H5Aclose(aid) < 0)
             TEST_ERROR
diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c
index 123263c..3d9472a 100644
--- a/tools/src/h5repack/h5repack_filters.c
+++ b/tools/src/h5repack/h5repack_filters.c
@@ -338,9 +338,10 @@ int apply_filters(const char* name, /* object name from traverse list */
 
             sm_nbytes = msize;
             for (i = rank; i > 0; --i) {
+                hsize_t size = 0;
                 if(sm_nbytes == 0)
                     HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "number of bytes per stripmine must be > 0");
-                hsize_t size = H5TOOLS_BUFSIZE / sm_nbytes;
+                size = H5TOOLS_BUFSIZE / sm_nbytes;
                 if (size == 0) /* datum size > H5TOOLS_BUFSIZE */
                     size = 1;
                 sm_size[i - 1] = MIN(dims[i - 1], size);