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[pkgsrc/trunk]: pkgsrc/devel/hdf5 hdf5: Update to 1.10.6
details: https://anonhg.NetBSD.org/pkgsrc/rev/9a3bd1341ad5
branches: trunk
changeset: 347133:9a3bd1341ad5
user: nia <nia%pkgsrc.org@localhost>
date: Wed Jan 08 12:30:34 2020 +0000
description:
hdf5: Update to 1.10.6
New Features
============
Configuration:
-------------
- Update CMake for VS2019 support
CMake added support for VS2019 in version 3.15. Changes to the CMake
generator setting required changes to scripts. Also updated version
references in CMake files as necessary.
(ADB - 2019/11/18, HDFFV-10962)
- Update CMake options to match new autotools options
Add configure options (autotools - CMake):
enable-asserts HDF5_ENABLE_ASSERTS
enable-symbols HDF5_ENABLE_SYMBOLS
enable-profiling HDF5_ENABLE_PROFILING
enable-optimization HDF5_ENABLE_OPTIMIZATION
In addition NDEBUG is no longer forced defined and relies on the CMake
process.
(ADB - 2019/10/07, HDFFV-100901, HDFFV-10637, TRILAB-97)
- Update CMake tests to use FIXTURES
CMake test fixtures allow setup/cleanup tests and other dependency
requirements as properties for tests. This is more flexible for
modern CMake code.
(ADB - 2019/07/23, HDFFV-10529)
- Windows PDB files are always installed
There are build configuration or flag settings for Windows that may not
generate PDB files. If those files are not generated then the install
utility will fail because those PDB files are not found. An optional
variable, DISABLE_PDB_FILES, was added to not install PDB files.
(ADB - 2019/07/17, HDFFV-10424)
- Add mingw CMake support with a toolchain file
There have been a number of mingw issues that have been linked under
HDFFV-10845. It has been decided to implement the CMake cross-compiling
technique of toolchain files. We will use a linux platform with the mingw
compiler stack for testing. Only the C language is fully supported, and
the error tests are skipped. The C++ language works for static but shared
builds have a shared library issue with the mingw Standard Exception Handling
library, which is not available on Windows. Fortran has a common cross-compile
problem with the fortran configure tests.
(ADB - 2019/07/12, HDFFV-10845, HDFFV-10595)
- Windows PDB files are installed incorrectly
For static builds, the PDB files for windows should be installed next
to the static libraries in the lib folder. Also the debug versions of
libraries and PDB files are now correctly built using the default
CMAKE_DEBUG_POSTFIX setting.
(ADB - 2019/07/09, HDFFV-10581)
- Add option to build only shared libs
A request was made to prevent building static libraries and only build
shared. A new option was added to CMake, ONLY_SHARED_LIBS, which will
skip building static libraries. Certain utility functions will build with
static libs but are not published. Tests are adjusted to use the correct
libraries depending on SHARED/STATIC settings.
(ADB - 2019/06/12, HDFFV-10805)
- Add options to enable or disable building tools and tests
Configure options --enable-tests and --enable-tools were added for
autotools configure. These options are enabled by default, and can be
disabled with either --disable-tests (or tools) or --enable-tests=no
(or --enable-tools=no). Build time is reduced ~20% when tools are
disabled, 35% when tests are disabled, 45% when both are disabled.
Re-enabling them after the initial build requires running configure
again with the option(s) enabled.
(LRK - 2019/06/12, HDFFV-9976)
- Change tools tests to search the error stack
There are some use cases which can cause the error stack of tools to be
different then the expected output. These tests now use grepTest.cmake;
this was changed to allow the error file to be searched for an expected string.
(ADB - 2019/04/15, HDFFV-10741)
Library:
--------
- Added S3 and HDFS Virtual File Drivers (VFDs) to HDF5
These new VFDs have been introduced in HDF5-1.10.6. Instructions to
enable them when configuring HDF5 on Linux and Mac may be found at
https://portal.hdfgroup.org/display/HDF5/Virtual+File+Drivers+-+S3+and+HDFS.
Installing on Windows requires CMake 3.13 and the following additional setup.
Install openssl library (with dev files);
from "Shining Light Productions". msi package preferred.
PATH should have been updated with the installation dir.
set ENV variable OPENSSL_ROOT_DIR to the installation dir.
set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg
Install libcurl library (with dev files);
download the latest released version using git: https://github.com/curl/curl.git
Open a Visual Studio Command prompt
change to the libcurl root folder
run the "buildconf.bat" batch file
change to the winbuild directory
nmake /f Makefile.vc mode=dll MACHINE=x64
copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir)
set ENV variable CURL_ROOT to C:\curl (installation dir)
update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir).
the aws credentials file should be in %USERPROFILE%\.aws folder
set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3";
(ADB - 2019/09/12, HDFFV-10854)
C++ Library:
------------
- Added new wrappers for H5Pset/get_create_intermediate_group()
LinkCreatPropList::setCreateIntermediateGroup()
LinkCreatPropList::getCreateIntermediateGroup()
(BMR - 2019/04/22, HDFFV-10622)
Java Library:
----------------
- Fixed a failure in JUnit-TestH5P on 32-bit architectures
(JTH - 2019/04/30)
Support for new platforms, languages and compilers.
=======================================
- CMake added support for VS2019 in version 3.15. Updated scripts.
- macOS 10.13.6 Darwin 17.7.0 with Apple clang LLVM version 10.0.0
- macOS 10.14.6 Darwin 18.7.0 with Apple clang LLVM version 10.0.1
Bug Fixes since HDF5-1.10.5 release
==================================
Library
-------
- Improved performance when creating a large number of small datasets by
retrieving default property values from the API context instead of doing
skip list searches. More work is required to achieve parity with HDF5 1.8.
(CJH - 2019/12/10, HDFFV-10658)
- Fixed user-created data access properties not existing in the property list
returned by H5Dget_access_plist. Thanks to Steven Varga for submitting a
reproducer and a patch.
(CJH - 2019/12/9, HDFFV-10934)
- Inappropriate linking with deprecated MPI C++ libraries
HDF5 does not define *_SKIP_MPICXX in the public headers, so applications
can inadvertently wind up linking to the deprecated MPI C++ wrappers.
MPICH_SKIP_MPICXX and OMPI_SKIP_MPICXX have both been defined in H5public.h
so this should no longer be an issue. HDF5 makes no use of the deprecated
MPI C++ wrappers.
(DER - 2019/09/17, HDFFV-10893)
- fcntl(2)-based file locking incorrectly passed the lock argument struct
instead of a pointer to the struct, causing errors on systems where
flock(2) is not available.
File locking is used when files are opened to enforce SWMR semantics. A
lock operation takes place on all file opens unless the
HDF5_USE_FILE_LOCKING environment variable is set to the string "FALSE".
flock(2) is preferentially used, with fcntl(2) locks as a backup if
flock(2) is unavailable on a system (if neither is available, the lock
operation fails). On these systems, the file lock will often fail, which
causes HDF5 to not open the file and report an error.
This bug only affects POSIX systems. Win32 builds on Windows use a no-op
locking call which always succeeds. Systems which exhibit this bug will
have H5_HAVE_FCNTL defined but not H5_HAVE_FLOCK in the configure output.
This bug affects HDF5 1.10.0 through 1.10.5.
fcntl(2)-based file locking now correctly passes the struct pointer.
(DER - 2019/08/27, HDFFV-10892)
- Fixed a bug caused by a bad tag value when condensing object header
messages
There was an assertion failure when moving messages from running a
user test program with library release HDF5 1.10.4. It was because
the tag value (object header's address) was not set up when entering
the library routine H5O__chunk_update_idx(), which eventually
verifies the metadata tag value when protecting the object header.
The problem was fixed by replacing FUNC_ENTER_PACKAGE in H5O__chunk_update_idx()
with FUNC_ENTER_PACKAGE_TAG(oh->cache_info.addr) to set up the metadata tag.
(VC - 2019/08/23, HDFFV-10873)
- Fixed the test failure from test_metadata_read_retry_info() in
test/swmr.c
The test failure is due to an incorrect number of bins returned for
retry info (info.nbins). The # of bins expected for 101 read attempts
is 3 instead of 2. The routine H5F_set_retries() in src/H5Fint.c
calculates the # of bins by first obtaining the log10 value for
(read attempts - 1). For PGI/19, the log10 value for 100 read attempts
is 1.9999999999999998 instead of 2.00000. When casting the log10 value
to unsigned later on, the decimal part is chopped off causing the test
failure.
This was fixed by obtaining the rounded integer value (HDceil) for the
log10 value of read attempts first before casting the result to unsigned.
(VC - 2019/8/14, HDFFV-10813)
- Fixed an issue when creating a file with non-default file space info
together with library high bound setting to H5F_LIBVER_V18.
When setting non-default file space info in fcpl via
H5Pset_file_space_strategy() and then creating a file with both high and
low library bounds set to H5F_LIBVER_V18 in fapl, the library succeeds in
creating the file. File creation should fail because the feature of
setting non-default file space info does not exist in library release 1.8
or earlier.
This was fixed by setting and checking the proper version in the file
space info message based on the library low and high bounds when creating
and opening the HDF5 file.
(VC - 2019/6/25, HDFFV-10808)
- Fixed an issue where copying a version 1.8 dataset between files using
H5Ocopy fails due to an incompatible fill version
When using the HDF5 1.10.x H5Ocopy() API call to copy a version 1.8
dataset to a file created with both high and low library bounds set to
H5F_LIBVER_V18, the H5Ocopy() call will fail with the error stack indicating
that the fill value version is out of bounds.
This was fixed by changing the fill value message version to H5O_FILL_VERSION_3
(from H5O_FILL_VERSION_2) for H5F_LIBVER_V18.
(VC - 2019/6/14, HDFFV-10800)
- Fixed a bug that would cause an error or cause fill values to be
incorrectly read from a chunked dataset using the "single chunk" index if
the data was held in cache and there was no data on disk.
(NAF - 2019/03/06)
- Fixed a bug that could cause an error or cause fill values to be
incorrectly read from a dataset that was written to using H5Dwrite_chunk
if the dataset was not closed after writing.
(NAF - 2019/03/06, HDFFV-10716)
- Fixed memory leak in scale offset filter
In a special case where the MinBits is the same as the number of bits in
the datatype's precision, the filter's data buffer was not freed, causing
the memory usage to grow. In general the buffer was freed correctly. The
Minbits are the minimal number of bits to store the data values. Please
see the reference manual for H5Pset_scaleoffset for the details.
(RL - 2019/3/4, HDFFV-10705)
Configuration
-------------
- Correct option for default API version
CMake options for default API version are not mutually exclusive.
Change the multiple BOOL options to a single STRING option with the
strings; v16, v18, v110.
(ADB - 2019/08/12, HDFFV-10879)
Tools
-----
- h5repack was fixed to repack datasets with external storage
to other types of storage.
New test added to repack files and verify the correct data using h5diff.
(JS - 2019/09/25, HDFFV-10408)
(ADB - 2019/10/02, HDFFV-10918)
diffstat:
devel/hdf5/Makefile | 8 +-------
devel/hdf5/Makefile.common | 4 ++--
devel/hdf5/PLIST | 4 +++-
devel/hdf5/distinfo | 13 +++++++------
devel/hdf5/patches/patch-tools_test_h5jam_testh5jam.sh.in | 6 +++---
5 files changed, 16 insertions(+), 19 deletions(-)
diffs (103 lines):
diff -r a0c48ea84415 -r 9a3bd1341ad5 devel/hdf5/Makefile
--- a/devel/hdf5/Makefile Wed Jan 08 12:12:23 2020 +0000
+++ b/devel/hdf5/Makefile Wed Jan 08 12:30:34 2020 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.52 2019/10/06 12:05:33 nia Exp $
+# $NetBSD: Makefile,v 1.53 2020/01/08 12:30:34 nia Exp $
COMMENT= Hierarchical Data Format (new generation)
@@ -7,12 +7,6 @@
INSTALLATION_DIRS+= share/examples/hdf5/c
post-install:
- ${INSTALL_SCRIPT} ${WRKSRC}/tools/src/misc/h5cc \
- ${DESTDIR}${PREFIX}/bin/
- libtool --mode=install ${INSTALL_PROGRAM} ${WRKSRC}/tools/src/misc/h5clear \
- ${DESTDIR}${PREFIX}/bin/
- ${INSTALL_SCRIPT} ${WRKSRC}/tools/src/misc/h5redeploy.in \
- ${DESTDIR}${PREFIX}/bin/h5redeploy
cd ${WRKSRC} && ${INSTALL_DATA} COPYING \
release_docs/RELEASE.txt \
release_docs/HISTORY-1_10.txt \
diff -r a0c48ea84415 -r 9a3bd1341ad5 devel/hdf5/Makefile.common
--- a/devel/hdf5/Makefile.common Wed Jan 08 12:12:23 2020 +0000
+++ b/devel/hdf5/Makefile.common Wed Jan 08 12:30:34 2020 +0000
@@ -1,8 +1,8 @@
-# $NetBSD: Makefile.common,v 1.19 2019/10/06 12:05:33 nia Exp $
+# $NetBSD: Makefile.common,v 1.20 2020/01/08 12:30:34 nia Exp $
# used by devel/hdf5/Makefile
# used by devel/hdf5-c++/Makefile
-DISTNAME= hdf5-1.10.5
+DISTNAME= hdf5-1.10.6
CATEGORIES= devel
MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-${PKGVERSION_NOREV}/src/
EXTRACT_SUFX= .tar.bz2
diff -r a0c48ea84415 -r 9a3bd1341ad5 devel/hdf5/PLIST
--- a/devel/hdf5/PLIST Wed Jan 08 12:12:23 2020 +0000
+++ b/devel/hdf5/PLIST Wed Jan 08 12:30:34 2020 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.27 2019/10/06 12:05:33 nia Exp $
+@comment $NetBSD: PLIST,v 1.28 2020/01/08 12:30:34 nia Exp $
bin/gif2h5
bin/h52gif
bin/h5cc
@@ -30,11 +30,13 @@
include/H5FDcore.h
include/H5FDdirect.h
include/H5FDfamily.h
+include/H5FDhdfs.h
include/H5FDlog.h
include/H5FDmpi.h
include/H5FDmpio.h
include/H5FDmulti.h
include/H5FDpublic.h
+include/H5FDros3.h
include/H5FDsec2.h
include/H5FDstdio.h
include/H5FDwindows.h
diff -r a0c48ea84415 -r 9a3bd1341ad5 devel/hdf5/distinfo
--- a/devel/hdf5/distinfo Wed Jan 08 12:12:23 2020 +0000
+++ b/devel/hdf5/distinfo Wed Jan 08 12:30:34 2020 +0000
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.43 2019/10/06 12:05:33 nia Exp $
+$NetBSD: distinfo,v 1.44 2020/01/08 12:30:34 nia Exp $
-SHA1 (hdf5-1.10.5.tar.bz2) = 5adf73f080ebfda58e58dc5bce7500faa0d6738c
-RMD160 (hdf5-1.10.5.tar.bz2) = 1880b8688015540abb5d6a73221775d780c07155
-SHA512 (hdf5-1.10.5.tar.bz2) = 769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4
-Size (hdf5-1.10.5.tar.bz2) = 8706317 bytes
+SHA1 (hdf5-1.10.6.tar.bz2) = 5e11d91abe071858b0d9a4f3a202c1e6a0d27290
+RMD160 (hdf5-1.10.6.tar.bz2) = c31216cd83187e69509fa36c6ae7015cee331ea1
+SHA512 (hdf5-1.10.6.tar.bz2) = 821392718605e3f7a287d4729d022a55fd7b91ddaa2e9a3f35ab8fce3d3d4871a0cc88215be3052887cbac3615cc8953569c7f131217962103c98151c0ab58d4
+Size (hdf5-1.10.6.tar.bz2) = 8813699 bytes
SHA1 (patch-c++_examples_Makefile.in) = 2b62c0b30258fcce5e22b5932bd400ca5897e0c3
SHA1 (patch-c++_examples_run-c++-ex.sh.in) = 2575d749930773fbe58dd1394cc451ad88fd4ed3
SHA1 (patch-configure) = e7f141d54c39cbee2f7d703ab7d6ff582158904e
@@ -14,4 +14,5 @@
SHA1 (patch-hl_examples_Makefile.in) = df3650c121152471a045e1fec169eedeea757377
SHA1 (patch-hl_examples_run-hlc-ex.sh.in) = 43bf6c28fb667f3ae39145be08e0a3a75f370b47
SHA1 (patch-src_H5private.h) = dbf7e44248b653274fbe1e0f7429d723107c6cdd
-SHA1 (patch-tools_test_h5jam_testh5jam.sh.in) = c23e66454bf817b68120d360c63329ebed6ac2aa
+SHA1 (patch-tools_test_h5jam_testh5jam.sh.in) = 17c93dcd36556667383d8def13450a09b75d5623
+SHA1 (patch-tools_test_h5repack_h5repack.sh.in) = 03bfd89a55f618fcc7719ff0bb122419f562f598
diff -r a0c48ea84415 -r 9a3bd1341ad5 devel/hdf5/patches/patch-tools_test_h5jam_testh5jam.sh.in
--- a/devel/hdf5/patches/patch-tools_test_h5jam_testh5jam.sh.in Wed Jan 08 12:12:23 2020 +0000
+++ b/devel/hdf5/patches/patch-tools_test_h5jam_testh5jam.sh.in Wed Jan 08 12:30:34 2020 +0000
@@ -1,12 +1,12 @@
-$NetBSD: patch-tools_test_h5jam_testh5jam.sh.in,v 1.1 2017/11/15 20:28:27 minskim Exp $
+$NetBSD: patch-tools_test_h5jam_testh5jam.sh.in,v 1.2 2020/01/08 12:30:34 nia Exp $
Use portable "=" to test string equality.
---- tools/test/h5jam/testh5jam.sh.in.orig 2017-04-25 21:45:02.000000000 +0000
+--- tools/test/h5jam/testh5jam.sh.in.orig 2019-12-19 16:38:30.000000000 +0000
+++ tools/test/h5jam/testh5jam.sh.in
@@ -474,9 +474,9 @@ UNJAMTEST () {
#
-
+
TOOLTEST_OUTPUT() {
- if [ "$1" == "JAM" ]; then
+ if [ "$1" = "JAM" ]; then
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