Merge pull request #159 in HDFFV/hdf5 from hdf5_1_8_18 to 1.8/masterhdf5-1_8_18

* commit '6974764348a88590d1901f316f956893dfa223d8': (28 commits)
  Version string at top of README.txt and release_docs/RELEASE.txt updated by bin/release.
  Update URLs in RELEASE.txt.
  Set version and commit release script changes for 1.8.18 release.
  Update HDF5 document URLs in RELEASE.txt.
  Description:     Replaced an incorrect work-around note with info about future feature     to fix the problem.
  Change default build mode to production. Update version to 1.8.18-pre2.
  Update versions for actual 1.8.18-pre1 release.
  Add GIT note
  Updates to RELEASE.txt to account for changes in the 1.8.18 release
  Updates to RELEASE.txt to account for changes in the 1.8.18 release
  Updated optional CMake scripts
  Updates to RELEASE.txt to account for changes in the 1.8.18 release.
  Remove ADA machine no longer tested from "Supported Platforms". Correct typo:  missing '(' for Mac OS 10.11 compiler information.
  Updates to RELEASE.txt to account for changes in the 1.8.18 release.
  Add bin/compile, bin/depcomp and bin/missing which were changed to links by libtool.
  Rerun libtoolize with -cf, then reconfigure.
  Created pre1 release files.
  Check in ltmain.sh and m4 files after running libtoolize with version 2.4.6.
  Update Windows tested platforms information.
  Update shared object file numbers according to changes in v1.8.18 release. Update autotools and libtool versions. Run bin/reconfigure.
  ...

1 files changed, 184 insertions, 83 deletions

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index cc1b4e2..568a280 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -1,39 +1,39 @@
-HDF5 version 1.8.18-snap2 currently under development
+HDF5 version 1.8.18 released on 2016-11-14
 ================================================================================
 
 INTRODUCTION
 ============
 
 This document describes the differences between HDF5-1.8.17 and
-HDF5-1.8.18-*, and contains information on the platforms tested and
-known problems in HDF5-1.8.18-*.
+HDF5-1.8.18, and contains information on the platforms tested and
+known problems in HDF5-1.8.18.
 For more details, see the files HISTORY-1_0-1_8_0_rc3.txt
 and HISTORY-1_8.txt in the release_docs/ directory of the HDF5 source.
 
 Links to the HDF5 1.8.18 source code, documentation, and additional materials
 can be found on the HDF5 web page at:
 
-     http://www.hdfgroup.org/products/hdf5/
+     https://support.hdfgroup.org/HDF5/
 
 The HDF5 1.8.18 release can be obtained from:
 
-     http://www.hdfgroup.org/HDF5/release/obtain5.html
+     https://support.hdfgroup.org/HDF5/release/obtain518.html
 
 User documentation for 1.8.18 can be accessed directly at this location:
 
-     http://www.hdfgroup.org/HDF5/doc/
+     https://support.hdfgroup.org/HDF5/doc1.8/
 
 New features in the HDF5-1.8.x release series, including brief general
 descriptions of some new and modified APIs, are described in the "What's New
 in 1.8.0?" document:
 
-     http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
+     https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html
 
 All new and modified APIs are listed in detail in the "HDF5 Software Changes
 from Release to Release" document, in the section "Release 1.8.18 (current
 release) versus Release 1.8.17
 
-     http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html
+     https://support.hdfgroup.org/HDF5/doc1.8/ADGuide/Changes.html
 
 If you have any questions or comments, please send them to the HDF Help Desk:
 
@@ -57,23 +57,34 @@ New Features
 
     Configuration
     -------------
-    - CMake
-      Added NAMESPACE hdf5:: to package configuration files
-    - CMake: change CTEST_BUILD_CONFIGURATION to CTEST_CONFIGURATION_TYPE, which is
-      recommended by CMake documentation.
-      HDFFV-9971 (ADB 2016/8/22)
 
+    - CMake: Added NAMESPACE hdf5:: to package configuration files to allow
+      projects using installed HDF5 binaries built with CMake to link with
+      them without specifying the HDF5 library location via IMPORTED_LOCATION.
+
+      (ADB, 2016/10/17, HDFFV-10003)
+
+
+    - CMake: Changed the CTEST_BUILD_CONFIGURATION option to
+      CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation.
+
+      (ADB, 2016/10/17, HDFFV-9971)
+
+    - CMake: Added support for GIT
+
+      (ADB, 2016/07/12)
 
 
     Library
     -------
-    -None
+    - None
 
 
     Parallel Library
     ----------------
     - None
 
+
     Tools
     -----
     - None
@@ -81,9 +92,6 @@ New Features
 
     High-Level APIs
     ---------------
-
-    C Packet Table API
-    ------------------
     - None
 
 
@@ -99,37 +107,103 @@ New Features
 
 Support for New Platforms, Languages, and Compilers
 ===================================================
-    
-    
+
+
 
 Bug Fixes since HDF5-1.8.17
 ===========================
 
     Configuration
     -------------
-    - None
+
+    - Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by
+      condensing cygwin configuration files into a single file and
+      removing outdated compiler settings.
+
+      (ABD, 2016/07/12, HDFFV-9946)
+
+
+    - CMake: Fixed a command length overflow error by converting custom
+      commands inside CMakeTest.cmake files into regular dependencies and
+      targets.
+
+      (ABD, 2016/07/12, HDFFV-9939)
+
+
+    - CMake: Fixed a timeout error that would occasionally occur when running
+      the virtual file driver tests simultaneously due to test directory and file
+      name collisions.
+
+      (ABD, 2016/09/19, HDFFV-9431)
 
 
     Library
     -------
-    - Fixed a bug that could occur when using H5Pset_alignment.
+
+    - Fixed a memory leak that would occur when the library allocated memory
+      for an external file prefix (H5Pset_efile_prefix) and failed to free it.
+
+      (DER, 2016/04/29)
+
+
+    - Fixed an error that would occur when calling H5Adelete on an attribute
+      which is attached to an externally linked object in the target file and
+      whose datatype is a committed datatype in the main file.
+
+      (VC, 2016-07-04, HDFFV-9940)
+
+
+    - Fixed a problem where a plugin compiled into a DLL in the default plugin
+      directory could not be found by the HDF5 library at runtime on Windows
+      when the HDF5_PLUGIN_PATH environment variable was not set.
+
+      (ABD, 2016/08/01, HDFFV-9706)
+
+
+    - Fixed an issue where H5Pset_alignment could result in misaligned blocks
+      with some input combinations, causing an assertion failure in debug mode.
 
       (NAF, 2016/08/11, HDFFV-9948)
 
-    - Fixed a memory bug that could occur when a message was improperly marked
-      as sharable on disk.
 
-      (NAF, 2016/07/01, HDFFV-9950)
+    - A number of issues were fixed when reading/writing from/to corrupted
+      files to ensure that the library fails gracefully in these cases:
+
+      * Writing to a corrupted file that has an object message which is
+        incorrectly marked as sharable on disk results in a buffer overflow /
+        invalid write instead of a clean error message.
+
+      * Decoding data from a corrupted file with a dataset encoded with the
+        H5Z_NBIT decoding can result in a code execution vulnerability under
+        the context of the application using the HDF5 library.
+
+      * When decoding an array datatype from a corrupted file, the HDF5 library
+        fails to return an error in production if the number of dimensions
+        decoded is greater than the maximum rank.
+
+      * When decoding an "old style" array datatype from a corrupted file, the
+        HDF5 library fails to return an error in production if the number of
+        dimensions decoded is greater than the maximum rank.
+
+      (NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993)
+
+
+    - Fixed an error that would occur when copying an object with an attribute
+      which is a compound datatype consisting of a variable length string.
+
+      (VC, 2016-10-17, HDFFV-7991)
 
 
     Parallel Library
     ----------------
+
     - Fixed a bug that could occur when allocating a chunked dataset in parallel
       with an alignment set and an alignment threshold greater than the chunk
       size but less than or equal to the raw data aggregator size.
 
       (NAF, 2016/08/11, HDFFV-9969)
 
+
     Performance
     -------------
     - None
@@ -137,6 +211,15 @@ Bug Fixes since HDF5-1.8.17
 
     Tools
     -----
+
+    - Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.)
+      in which they would erroneously drop the file argument specified via
+      the -o flag when the -o flag was specified before the -c flag on the
+      command line, resulting in a failure to compile.
+
+      (LRK, 2016/06/08, HDFFV-9938, HDFFV-9530)
+
+
     - h5repack User Defined (UD) filter parameters were not parsed correctly.
 
       The UD filter parameters were not being parsed correctly. Reworked coding
@@ -147,17 +230,54 @@ Bug Fixes since HDF5-1.8.17
 
     Fortran API
     -----------
-    - None
+
+    - Fortran library fails to compile and fails tests with NAG compiler.
+
+      * Removed the non-standard assumption that KIND=SIZEOF, in the HDF5
+        configure programs.
+      * Removed Fortran 66 character/integer conversions from tests.
+      * Removed the use of C_SIZEOF in the test programs
+      * Changed to using STORAGE_SIZE in the test programs if available. Otherwise,
+        uses C_SIZEOF or SIZEOF.
+
+      (MSB, 2016/9/22, HDFFV-9973)
+
+
+    - Fortran segfaults for F03 tests with NAG compiler
+
+      * Removed INTENT(OUT) from 'fillvalue' in F2003 interface
+        for H5Pget_fill_value_f.
+
+      (MSB, 2016/9/22, HDFFV-9980)
 
 
     C++ API
     -------
-    - None
+
+    - The macro H5_NO_NAMESPACE is deprecated from the HDF5 C++ API library.
+      In future releases, the macros H5_NO_STD and OLD_HEADER_FILENAME may
+      also be removed.
+
+      (BMR, 2016/10/27, HDFFV-9532)
 
 
     High-Level APIs:
     ---------------
-    - None
+
+    - The high-level API Packet Table (PT) did not write data correctly when
+      the datatype is a compound type that has string type as one of the
+      members.  This problem started in 1.8.15, after the fix of HDFFV-9042
+      was applied, which caused the Packet Table to use native type to access
+      the data.  It should be up to the application to specify whether the
+      buffer to be read into memory in the machine’s native architecture.
+      Thus, the PT is fixed to not use native type but to make a copy of the
+      user's provided datatype during creation or the packet table's datatype
+      during opening.  If an application wishes to use native type to read the
+      data, then the application will request that.  However, the Packet Table
+      doesn't provide a way to specify memory datatype in this release.  This
+      feature will be available in future releases, HDFFV-10023.
+
+      (BMR, 2016/10/27, HDFFV-9758)
 
 
     Fortran High-Level APIs:
@@ -175,14 +295,10 @@ Supported Platforms
 The following platforms are supported and have been tested for this release.
 They are built with the configure process unless specified otherwise.
 
-    AIX 6.1                       xlc/xlc_r 10.1.0.5
-    (NASA G-ADA)                  xlC/xlC_r 10.1.0.5
-                                  xlf90/xlf90_r 12.1.0.6
-
-    Linux 2.6.32-573.3.1.el6    GNU C (gcc), Fortran (gfortran), C++ (g++)
+    Linux 2.6.32-573.22.1.el6     GNU C (gcc), Fortran (gfortran), C++ (g++)
     #1 SMP x86_64 GNU/Linux       compilers:
-    (platypus)                       Version 4.4.7 20120313
-                                     Version 4.8.4, Version 5.2.0
+    (platypus/mayll)              Version 4.4.7 20120313
+                                     Versions 4.8.4, 4.9.3, 5.2.0
                                   PGI C, Fortran, C++ for 64-bit target on
                                   x86-64;
                                       Version 15.7-0
@@ -191,16 +307,16 @@ They are built with the configure process unless specified otherwise.
                                      Version 15.0.3.187 Build 20150407
                                   MPICH 3.1.4 compiled with GCC 4.9.3
 
-    Linux 2.6.32-504.8.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
-    #1 SMP ppc64 GNU/Linux        g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
-    (ostrich)                     GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-11)
+    Linux 2.6.32-573.18.1.el6     gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
+    #1 SMP ppc64 GNU/Linux        g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
+    (ostrich)                     GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
                                   IBM XL C/C++ V13.1
                                   IBM XL Fortran V15.1
 
-    Linux 3.10.0-229.14.1.el7   GNU C (gcc), Fortran (gfortran), C++ (g++)
+    Linux 3.10.0-327.10.1.el7     GNU C (gcc), Fortran (gfortran), C++ (g++)
     #1 SMP x86_64 GNU/Linux       compilers:
-    (kituo/moohan)                  Version 4.8.3 20140911 (Red Hat 4.8.3-9)
-                                    Version 5.2.0
+    (kituo/moohan)                  Version 4.8.5 20150623 (Red Hat 4.8.5-4)
+                                    Versions 4.9.3, 5.2.0
                                   Intel(R) C (icc), C++ (icpc), Fortran (icc)
                                   compilers:
                                      Version 15.0.3.187 Build 20150407
@@ -220,24 +336,26 @@ They are built with the configure process unless specified otherwise.
                                   Visual Studio 2013 w/ Intel Fortran 15 (cmake)
                                   Visual Studio 2015 w/ Intel Fortran 16  (cmake)
 
-    Windows 8.1                   Visual Studio 2012 w/ Intel Fortran 15 (cmake)
-                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)
+    Windows 10                    Visual Studio 2015 w/ Intel Fortran 16 (cmake)
 
-    Windows 8.1 x64               Visual Studio 2012 w/ Intel Fortran 15 (cmake)
-                                  Visual Studio 2013 w/ Intel Fortran 15 (cmake)
+    Windows 10 x64                Visual Studio 2015 w/ Intel Fortran 16 (cmake)
 
-    Mac OS X Mt. Lion 10.8.5      Apple clang/clang++ version 5.1 from Xcode 5.1
+    Mac OS X Mt. Lion 10.8.5      Apple LLVM version 5.1 (clang-503.0.40)
     64-bit                        gfortran GNU Fortran (GCC) 4.8.2
     (swallow/kite)                Intel icc/icpc/ifort version 15.0.3
 
-    Mac OS X Mavericks 10.9.5     Apple clang/clang++ version 6.0 from Xcode 6.2.0
+    Mac OS X Mavericks 10.9.5     Apple LLVM version 6.0 (clang-600.0.57)
     64-bit                        gfortran GNU Fortran (GCC) 4.9.2
     (wren/quail)                  Intel icc/icpc/ifort version 15.0.3
 
-    Mac OS X Yosemite 10.10.5     Apple clang/clang++ version 6.0 from Xcode 7.0.0
+    Mac OS X Yosemite 10.10.5     Apple LLVM version 6.1 (clang-602.0.53)
     64-bit                        gfortran GNU Fortran (GCC) 4.9.2
     (osx1010dev/osx1010test)      Intel icc/icpc/ifort version 15.0.3
 
+    Mac OS X El Capitan 10.11.4   Apple LLVM version 7.3.0 (clang-703.0.29)
+    64-bit                        gfortran GNU Fortran (GCC) 5.2.0
+    (VM osx1011dev/osx1011test)   Intel icc/icpc/ifort version 16.0.2
+
 
 Tested Configuration Features Summary
 =====================================
@@ -259,11 +377,11 @@ SunOS 5.11 64-bit                       n        y/y    n        y    y     y
 Windows 7                               y        y/y    n        y    y     y
 Windows 7 x64                           y        y/y    n        y    y     y
 Windows 7 Cygwin                        n        y/y    n        y    y     n
-Windows 8.1                             n        y/y    n        y    y     y
-Windows 8.1 x64                         n        y/y    n        y    y     y
+Windows 10                              n        y/y    n        y    y     y
+Windows 10 x64                          n        y/y    n        y    y     y
 Mac OS X Mountain Lion 10.8.5 64-bit    n        y/y    n        y    y     y
 Mac OS X Mavericks 10.9.5 64-bit        n        y/y    n        y    y     y
-Mac OS X Yosemeti 10.10.5 64-bit        n        y/y    n        y    y     y
+Mac OS X Yosemite 10.10.5 64-bit        n        y/y    n        y    y     y
 AIX 6.1 32- and 64-bit                  n        y/n    n        y    y     y
 CentOS 6.7 Linux 2.6.32 x86_64 GNU      y        y/y    y        y    y     y
 CentOS 6.7 Linux 2.6.32 x86_64 Intel    n        y/y    n        y    y     y
@@ -279,11 +397,11 @@ SunOS 5.11 64-bit                          y       y         y         y
 Windows 7                                  y       y         y         y
 Windows 7 x64                              y       y         y         y
 Windows 7 Cygwin                           n       n         n         y
-Windows 8.1                                y       y         y         y
-Windows 8.1 x64                            y       y         y         y
+Windows 10                                 y       y         y         y
+Windows 10 x64                             y       y         y         y
 Mac OS X Mountain Lion 10.8.5 64-bit       y       n         y         y
 Mac OS X Mavericks 10.9.5 64-bit           y       n         y         y
-Mac OS X Yosemeti 10.10.5 64-bit           y       n         y         y
+Mac OS X Yosemite 10.10.5 64-bit           y       n         y         y
 AIX 6.1 32- and 64-bit                     y       n         n         y
 CentOS 6.7 Linux 2.6.32 x86_64 GNU         y       y         y         y
 CentOS 6.7 Linux 2.6.32 x86_64 Intel       y       y         y         y
@@ -300,47 +418,30 @@ More Tested Platforms
 =====================
 The following platforms are not supported but have been tested for this release.
 
-    Linux 2.6.18-431.11.2.el6     g95 (GCC 4.0.3 (g95 0.94!)
+    Linux 2.6.32-573.22.1.el6     g95 (GCC 4.0.3 (g95 0.94!)
     #1 SMP x86_64 GNU/Linux
     (platypus)
 
-    Mac OS X El Capitan 10.11     Apple clang/clang++ version 7.0.0 from Xcode 7.0.1
-    64-bit                        gfortran GNU Fortran (GCC) 5.2.0
-    (VM)
-
-    Windows 7                     Visual Studio 2008  (cmake)
-
-    Windows 7 x64                 Visual Studio 2008  (cmake)
-
-    Windows 10                    Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
-    Windows 10 x64                Visual Studio 2013 w/ Intel Fortran 15 (cmake)
-
-    Debian7.5.0 3.2.0-4-amd64 #1 SMP Debian 3.2.51-1 x86_64 GNU/Linux
-                                  gcc (Debian 4.7.2-5) 4.7.2
-                                  GNU Fortran (Debian 4.7.2-5) 4.7.2
+    Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
+                                  gcc (Debian 4.9.2-10) 4.9.2
+                                  GNU Fortran (Debian 4.9.2-10) 4.9.2
                                   (cmake and autotools)
 
-    Fedora20 3.15.3-200.fc20.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
-                                  gcc (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
-                                  GNU Fortran (GCC) 4.8.3 20140624 (Red Hat 4.8.3-1)
+    Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
+                                  gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
+                                  GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
                                   (cmake and autotools)
 
-    SUSE 13.1 3.11.10-17-desktop #1 SMP PREEMPT x86_64 x86_64 x86_64 GNU/Linux
-                                  gcc (SUSE Linux) 4.8.1
-                                  GNU Fortran (SUSE Linux) 4.8.1
+    CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
+                                  gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
+                                  GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
                                   (cmake and autotools)
 
-    Ubuntu 14.04 3.13.0-35-generic #62-Ubuntu SMP x86_64 GNU/Linux
-                                  gcc (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
-                                  GNU Fortran (Ubuntu/Linaro 4.9.1-0ubuntu1) 4.9.1
+    Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux
+                                  gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
+                                  GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
                                   (cmake and autotools)
 
-    hopper.nersc.gov              PrgEnv-gnu/5.2.40
-                                  gcc (GCC) 4.9.2 20141030 (Cray Inc.)
-                                  GNU Fortran (GCC) 4.9.2 20141030 (Cray Inc.)
-                                  g++ (GCC) 4.9.2 20141030 (Cray Inc.)
-
 
 Known Problems
 ==============