[svn-r27850] Description:

    Sync w/trunk

Tested on:
    MacOSX/64 10.10.5 (amazon) w/serial
    (h5committest not required on this branch)

10 files changed, 142 insertions, 82 deletions

diff --git a/MANIFEST b/MANIFEST
index 030c3a6..8321a2a 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -2402,6 +2402,7 @@
 ./config/cmake/hdf5-config.cmake.in
 ./config/cmake/hdf5-config-version.cmake.in
 ./config/cmake/HDFCompilerFlags.cmake
+./config/cmake/HDF5_Process_Flex_Files.cmake
 ./config/cmake/HDF5Macros.cmake
 ./config/cmake/HDF5UseFortran.cmake
 ./config/cmake/libhdf5.settings.cmake.in
diff --git a/config/cmake/HDF5Macros.cmake b/config/cmake/HDF5Macros.cmake
index 9b36f53..bd86f34 100644
--- a/config/cmake/HDF5Macros.cmake
+++ b/config/cmake/HDF5Macros.cmake
@@ -39,75 +39,4 @@ macro (H5_SET_LIB_OPTIONS libtarget libname libtype)
       endif (${libtype} MATCHES "SHARED")
     endif (HDF5_BUILD_FRAMEWORKS)
   endif (APPLE)
-
 endmacro (H5_SET_LIB_OPTIONS)
-
-macro (H5_GEN_PERL_FILES)
-  find_package (Perl)
-  if (PERL_FOUND)
-    add_custom_command (
-        OUTPUT ${HDF5_BINARY_DIR}/H5Edefin.h
-        PRE_BUILD
-        COMMAND ${PERL_EXECUTABLE}
-        ARGS ${HDF5_SOURCE_DIR}/bin/make_err ${HDF5_SOURCE_DIR}/src/H5err.txt
-        DEPENDS ${HDF5_SOURCE_DIR}/src/H5err.txt
-        COMMENT " Creating err header"
-    )
-
-    add_custom_command (
-        OUTPUT ${HDF5_BINARY_DIR}/H5version.h
-        PRE_BUILD
-        COMMAND ${PERL_EXECUTABLE}
-        ARGS ${HDF5_SOURCE_DIR}/bin/make_vers  ${HDF5_SOURCE_DIR}/src/H5vers.txt
-        DEPENDS ${HDF5_SOURCE_DIR}/src/H5vers.txt
-       COMMENT " Creating API version macro"
-    )
-
-    add_custom_command (
-        OUTPUT ${HDF5_BINARY_DIR}/H5overflow.h
-        PRE_BUILD
-        COMMAND ${PERL_EXECUTABLE}
-        ARGS ${HDF5_SOURCE_DIR}/bin/make_overflow  ${HDF5_SOURCE_DIR}/src/H5overflow.txt
-        DEPENDS ${HDF5_SOURCE_DIR}/src/H5overflow.txt
-        COMMENT " Creating Assignment overflow macro"
-    )
-
-    add_custom_target(run_perl_scripts ALL
-        DEPENDS ${HDF5_BINARY_DIR}/H5Edefin.h ${HDF5_BINARY_DIR}/H5version.h ${HDF5_BINARY_DIR}/H5overflow.h
-    )
-  else (PERL_FOUND)
-    message (STATUS "Cannot generate headers - perl not found")
-  endif (PERL_FOUND)
-endmacro (H5_GEN_PERL_FILES)
-
-macro (H5_GEN_FLEX_FILES)
-  find_package (BISON)
-  if (BISON_FOUND)
-    find_package (FLEX)
-    if (FLEX_FOUND)
-      BISON_TARGET (H5LT_PARSER H5LTparse.y ${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.c COMPILE_FLAGS -d)
-      if (WIN32)
-        FLEX_TARGET (H5LT_SCANNER H5LTanalyze.l ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c COMPILE_FLAGS --wincompat)
-      else (WIN32)
-        FLEX_TARGET (H5LT_SCANNER H5LTanalyze.l ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c)
-      endif (WIN32)
-      ADD_FLEX_BISON_DEPENDENCY(H5LT_SCANNER H5LT_PARSER)
-
-      if (BISON_H5LT_PARSER_DEFINED AND FLEX_H5LT_SCANNER_DEFINED)
-        set_source_files_properties (${FLEX_H5LT_SCANNER_OUTPUTS}
-            PROPERTIES OBJECT_DEPENDS ${BISON_H5LT_PARSER_OUTPUTS})
-        set (HL_SRCS
-            ${BISON_H5LT_PARSER_OUTPUTS}
-            ${FLEX_H5LT_SCANNER_OUTPUTS}
-        )
-        include_directories(${CMAKE_CURRENT_BINARY_DIR})
-      else (BISON_H5LT_PARSER_DEFINED AND FLEX_H5LT_SCANNER_DEFINED)
-        message (STATUS "Error during generate of files")
-      endif (BISON_H5LT_PARSER_DEFINED AND FLEX_H5LT_SCANNER_DEFINED)
-    else (FLEX_FOUND)
-      message (STATUS "Cannot generate files - flex not found")
-    endif (FLEX_FOUND)
-  else (BISON_FOUND)
-    message (STATUS "Cannot generate files - bison not found")
-  endif (BISON_FOUND)
-endmacro (H5_GEN_FLEX_FILES)
diff --git a/config/cmake/HDF5_Process_Flex_Files.cmake b/config/cmake/HDF5_Process_Flex_Files.cmake
new file mode 100644
index 0000000..da1a842
--- /dev/null
+++ b/config/cmake/HDF5_Process_Flex_Files.cmake
@@ -0,0 +1,81 @@
+# post process flex/bison files
+
+message (STATUS "File: ${FILE_PARSE} ${FILE_ANALYZE}")
+
+if (FILE_PARSE)
+  # fix H5LTparse.c to declare H5LTyyparse return type as an hid_t
+  # instead of int.  Currently the generated function H5LTyyparse is
+  # generated with a return value of type int, which is a mapping to the
+  # flex yyparse function.  The return value in the HL library should be
+  # an hid_t.
+  # I propose to not use flex to generate this function, but for now I am
+  # adding a perl command to find and replace this function declaration in
+  # H5LTparse.c.
+    file (READ ${FILE_PARSE} TEST_STREAM)
+    string (REGEX REPLACE "int\nyyparse" "hid_t\nyyparse" TEST_STREAM "${TEST_STREAM}")
+    string (REGEX REPLACE "int H5LTyyparse" "hid_t H5LTyyparse" TEST_STREAM "${TEST_STREAM}")
+    file (WRITE ${FILE_PARSE} "${TEST_STREAM}")
+    message (STATUS "replacing signature in H5LTparse.c")
+
+  # Add code that disables warnings in the flex/bison-generated code.
+  #
+  # Note that the GCC pragmas did not exist until gcc 4.2. Earlier versions
+  # will simply ignore them, but we want to avoid those warnings.
+    file (READ ${FILE_PARSE} TEST_STREAM)
+    file (WRITE ${FILE_PARSE} "
+#if __GNUC__ >= 4 && __GNUC_MINOR__ >=2\n
+#pragma GCC diagnostic ignored \"-Wconversion\"\n
+#pragma GCC diagnostic ignored \"-Wimplicit-function-declaration\"\n
+#pragma GCC diagnostic ignored \"-Wlarger-than=\"\n
+#pragma GCC diagnostic ignored \"-Wmissing-prototypes\"\n
+#pragma GCC diagnostic ignored \"-Wnested-externs\"\n
+#pragma GCC diagnostic ignored \"-Wold-style-definition\"\n
+#pragma GCC diagnostic ignored \"-Wsign-compare\"\n
+#pragma GCC diagnostic ignored \"-Wsign-conversion\"\n
+#pragma GCC diagnostic ignored \"-Wstrict-prototypes\"\n
+#pragma GCC diagnostic ignored \"-Wswitch-default\"\n
+#pragma GCC diagnostic ignored \"-Wunused-function\"\n
+#pragma GCC diagnostic ignored \"-Wunused-macros\"\n
+#pragma GCC diagnostic ignored \"-Wunused-parameter\"\n
+#pragma GCC diagnostic ignored \"-Wredundant-decls\"\n
+#elif defined __SUNPRO_CC\n
+#pragma disable_warn\n
+#elif defined _MSC_VER\n
+#pragma warning(push, 1)\n
+#endif\n
+    ")
+    file (APPEND ${FILE_PARSE} "${TEST_STREAM}")
+    message (STATUS "processing pragma in ${FILE_PARSE}")
+endif (FILE_PARSE)
+
+if (FILE_ANALYZE)
+  # Add code that disables warnings in the flex/bison-generated code.
+  #
+  # Note that the GCC pragmas did not exist until gcc 4.2. Earlier versions
+  # will simply ignore them, but we want to avoid those warnings.
+    file (READ ${FILE_ANALYZE} TEST_STREAM)
+    file (WRITE ${FILE_ANALYZE} "
+#if __GNUC__ >= 4 && __GNUC_MINOR__ >=2\n
+#pragma GCC diagnostic ignored \"-Wconversion\"\n
+#pragma GCC diagnostic ignored \"-Wimplicit-function-declaration\"\n
+#pragma GCC diagnostic ignored \"-Wlarger-than=\"\n
+#pragma GCC diagnostic ignored \"-Wmissing-prototypes\"\n
+#pragma GCC diagnostic ignored \"-Wnested-externs\"\n
+#pragma GCC diagnostic ignored \"-Wold-style-definition\"\n
+#pragma GCC diagnostic ignored \"-Wsign-compare\"\n
+#pragma GCC diagnostic ignored \"-Wsign-conversion\"\n
+#pragma GCC diagnostic ignored \"-Wstrict-prototypes\"\n
+#pragma GCC diagnostic ignored \"-Wswitch-default\"\n
+#pragma GCC diagnostic ignored \"-Wunused-function\"\n
+#pragma GCC diagnostic ignored \"-Wunused-macros\"\n
+#pragma GCC diagnostic ignored \"-Wunused-parameter\"\n
+#pragma GCC diagnostic ignored \"-Wredundant-decls\"\n
+#elif defined __SUNPRO_CC\n
+#pragma disable_warn\n
+#elif defined _MSC_VER\n
+#pragma warning(push, 1)\n
+#endif\n
+    ")
+    file (APPEND ${FILE_ANALYZE} "${TEST_STREAM}")
+    message (STATUS "processing pragma in ${FILE_ANALYZE}")
+endif (FILE_ANALYZE)
diff --git a/config/cmake/cacheinit.cmake b/config/cmake/cacheinit.cmake
index e4ba880..4bef99f 100644
--- a/config/cmake/cacheinit.cmake
+++ b/config/cmake/cacheinit.cmake
@@ -8,8 +8,6 @@ set (CMAKE_INSTALL_FRAMEWORK_PREFIX "Library/Frameworks" CACHE STRING "Framework
 
 set (HDF_PACKAGE_EXT "" CACHE STRING "Name of HDF package extension" FORCE)
 
-set (HDF5_GENERATE_HEADERS ON CACHE BOOL "Rebuild Generated Files" FORCE)
-
 set (HDF5_BUILD_FORTRAN ON CACHE BOOL "Build FORTRAN support" FORCE)
 
 set (HDF5_BUILD_GENERATORS OFF CACHE BOOL "Build Test Generators" FORCE)
diff --git a/config/cmake/mccacheinit.cmake b/config/cmake/mccacheinit.cmake
index 7f981df..19ecc15 100644
--- a/config/cmake/mccacheinit.cmake
+++ b/config/cmake/mccacheinit.cmake
@@ -12,8 +12,6 @@ set (BUILD_TESTING ON CACHE BOOL "Build HDF5 Unit Testing" FORCE)
 
 set (HDF_PACKAGE_EXT "" CACHE STRING "Name of HDF package extension" FORCE)
 
-set (HDF5_GENERATE_HEADERS ON CACHE BOOL "Rebuild Generated Files" FORCE)
-
 set (HDF5_BUILD_CPP_LIB ON CACHE BOOL "Build HDF5 C++ Library" FORCE)
 
 set (HDF5_BUILD_EXAMPLES ON CACHE BOOL "Build HDF5 Library Examples" FORCE)
diff --git a/config/cmake/userblockTest.cmake b/config/cmake/userblockTest.cmake
index 2e0740b..fab470c 100644
--- a/config/cmake/userblockTest.cmake
+++ b/config/cmake/userblockTest.cmake
@@ -1,4 +1,4 @@
-# runTest.cmake executes a command and captures the output in a file. File is then compared
+# userblockTest.cmake executes a command and captures the output in a file. File is then compared
 # against a reference file. Exit status of command can also be compared.
 
 # arguments checking
@@ -56,9 +56,9 @@ if (TEST_CHECKUB STREQUAL "YES")
     endif (NOT ${TEST_RESULT} STREQUAL "0")
     file (READ ${TEST_HFILE}.len.txt TEST_O_STRING_LEN)
   endif (TEST_OFILE)
-   
+
   MATH( EXPR TEST_STRING_SIZE "${TEST_U_STRING_LEN} + ${TEST_O_STRING_LEN}" )
- 
+
   if (NOT TEST_O_STRING_LEN STREQUAL "0")
     #$JAM_BIN/getub -c $s2 $origfile > $cmpfile
     EXECUTE_PROCESS (
@@ -72,7 +72,7 @@ if (TEST_CHECKUB STREQUAL "YES")
     )
     #cat $ufile >> $cmpfile
     file (STRINGS ${TEST_UFILE} TEST_STREAM NEWLINE_CONSUME)
-    file (APPEND ${TEST_HFILE}-ub.cmp "${TEST_STREAM}") 
+    file (APPEND ${TEST_HFILE}-ub.cmp "${TEST_STREAM}")
   else (NOT TEST_O_STRING_LEN STREQUAL "0")
     file (STRINGS ${TEST_UFILE} TEST_STREAM NEWLINE_CONSUME)
     file (WRITE ${TEST_HFILE}-ub.cmp ${TEST_STREAM})
diff --git a/hl/src/CMakeLists.txt b/hl/src/CMakeLists.txt
index 8d1a37f..25f3cb5 100644
--- a/hl/src/CMakeLists.txt
+++ b/hl/src/CMakeLists.txt
@@ -26,6 +26,35 @@ if (HDF5_GENERATE_HEADERS)
         set_source_files_properties (${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c GENERATED)
         set_source_files_properties (${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.c GENERATED)
         set_source_files_properties (${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.h GENERATED)
+
+        add_custom_command (
+            OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.timestamp
+            COMMAND "${CMAKE_COMMAND}"
+                -D "FILE_PARSE=H5LTparse.c"
+                -P "${HDF_RESOURCES_DIR}/HDF5_Process_Flex_Files.cmake"
+            COMMAND ${CMAKE_COMMAND} -E touch ${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.timestamp
+            DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.c
+            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        )
+        add_custom_command (
+            OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.timestamp
+            COMMAND "${CMAKE_COMMAND}"
+                -D "FILE_ANALYZE=H5LTanalyze.c"
+                -P "${HDF_RESOURCES_DIR}/HDF5_Process_Flex_Files.cmake"
+            COMMAND ${CMAKE_COMMAND} -E touch ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.timestamp
+            DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c
+            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        )
+        add_custom_target (process_gen_H5LT DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.timestamp ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.timestamp)
+
+#        add_custom_target (process_gen_H5LT
+#            COMMAND "${CMAKE_COMMAND}"
+#              -D "FILE_PARSE=${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.c"
+#              -D "FILE_ANALYSE=${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c"
+#              -P "${HDF5_RESOURCE_DIR}/HDF5_Process_Flex_Files.cmake"
+#              DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/H5LTparse.c ${CMAKE_CURRENT_BINARY_DIR}/H5LTanalyze.c"
+#              COMMENT "Prepending pragma statements"
+#        )
       else (BISON_H5LT_PARSER_DEFINED AND FLEX_H5LT_SCANNER_DEFINED)
         message (STATUS "Error during generate of files")
       endif (BISON_H5LT_PARSER_DEFINED AND FLEX_H5LT_SCANNER_DEFINED)
@@ -82,6 +111,11 @@ set_target_properties (${HDF5_HL_LIB_TARGET} PROPERTIES
 )
 set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_LIB_TARGET}")
 set (install_targets ${HDF5_HL_LIB_TARGET})
+if (HDF5_GENERATE_HEADERS)
+  add_dependencies(${HDF5_HL_LIB_TARGET} process_gen_H5LT)
+else (HDF5_GENERATE_HEADERS)
+  add_dependencies(${HDF5_HL_LIB_TARGET} "${HDF5_HL_SRC_SOURCE_DIR}/H5LTanalyze.c;${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.c")
+endif (HDF5_GENERATE_HEADERS)
 
 if (BUILD_SHARED_LIBS)
   add_library (${HDF5_HL_LIBSH_TARGET} SHARED ${HL_SRCS} ${HL_HEADERS})
@@ -96,6 +130,11 @@ if (BUILD_SHARED_LIBS)
   )
   set_global_variable (HDF5_LIBRARIES_TO_EXPORT "${HDF5_LIBRARIES_TO_EXPORT};${HDF5_HL_LIBSH_TARGET}")
   set (install_targets ${install_targets} ${HDF5_HL_LIBSH_TARGET})
+  if (HDF5_GENERATE_HEADERS)
+    add_dependencies(${HDF5_HL_LIBSH_TARGET} process_gen_H5LT)
+  else (HDF5_GENERATE_HEADERS)
+    add_dependencies(${HDF5_HL_LIBSH_TARGET} "${HDF5_HL_SRC_SOURCE_DIR}/H5LTanalyze.c;${HDF5_HL_SRC_SOURCE_DIR}/H5LTparse.c")
+  endif (HDF5_GENERATE_HEADERS)
 endif (BUILD_SHARED_LIBS)
 
 #-----------------------------------------------------------------------------
diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt
index df6291f..5cc9baf 100644
--- a/release_docs/INSTALL_CMake.txt
+++ b/release_docs/INSTALL_CMake.txt
@@ -33,6 +33,10 @@ CMake version
       The HDF5 1.8."X" product requires a minimum CMake version 3.1.0,
       where "X" is the current HDF5 release version.
 
+Note:
+   To change the install prefix from the platform defaults initialize
+   the CMake variable, CMAKE_INSTALL_PREFIX.
+
 
 ========================================================================
 II. Quick Step Building HDF5 Libraries with CMake Script Mode
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index fce59c2..79f47c7 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -777,6 +777,8 @@ set (H5_GENERATED_HEADERS
     ${HDF5_SRC_DIR}/H5overflow.h
 )
 
+option (HDF5_GENERATE_HEADERS "Rebuild Generated Files" ON)
+mark_as_advanced (HDF5_GENERATE_HEADERS)
 if (HDF5_GENERATE_HEADERS)
   find_package (Perl)
   if (PERL_FOUND)
@@ -827,7 +829,11 @@ TARGET_C_PROPERTIES (H5detect STATIC " " " ")
 if (MSVC OR MINGW)
   target_link_libraries (H5detect "ws2_32.lib")
 endif (MSVC OR MINGW)
-add_dependencies(H5detect generate_precompiled)
+if (HDF5_GENERATE_HEADERS)
+  add_dependencies(H5detect generate_precompiled)
+else (HDF5_GENERATE_HEADERS)
+  add_dependencies(H5detect "${HDF5_SRC_DIR}/H5version.h;${HDF5_SRC_DIR}/H5overflow.h")
+endif (HDF5_GENERATE_HEADERS)
 
 set (CMD $<TARGET_FILE:H5detect>)
 add_custom_command (
@@ -842,7 +848,11 @@ TARGET_C_PROPERTIES (H5make_libsettings STATIC " " " ")
 if (MSVC OR MINGW)
   target_link_libraries (H5make_libsettings "ws2_32.lib")
 endif (MSVC OR MINGW)
-add_dependencies(H5make_libsettings generate_precompiled)
+if (HDF5_GENERATE_HEADERS)
+  add_dependencies(H5detect generate_precompiled)
+else (HDF5_GENERATE_HEADERS)
+  add_dependencies(H5make_libsettings "${HDF5_SRC_DIR}/H5version.h;${HDF5_SRC_DIR}/H5overflow.h")
+endif (HDF5_GENERATE_HEADERS)
 
 set (CMD $<TARGET_FILE:H5make_libsettings>)
 add_custom_command (
diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index 11267b6..d66a30a 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -713,7 +713,7 @@ H5S_get_select_offset(const H5S_t *space, hsize_t *offset)
 int
 H5S_get_select_unlim_dim(const H5S_t *space)
 {
-    herr_t ret_value;        /* return value */
+    herr_t ret_value = FAIL;    /* Return value */
 
     FUNC_ENTER_NOAPI_NOINIT_NOERR