[gentoo-commits] repo/gentoo:master commit in: sci-libs/hdf5/files/

2023-06-13 Thread Andrew Ammerlaan 
commit: eed0d90c361035f9c51298398a0a1e9d0ec4cc68
Author: Michael Mair-Keimberger  levelnine  at>
AuthorDate: Tue Jun 13 16:48:12 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue Jun 13 19:48:48 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=eed0d90c

sci-libs/hdf5: remove unused patch

Signed-off-by: Michael Mair-Keimberger  levelnine.at>
Closes: https://github.com/gentoo/gentoo/pull/31426
Signed-off-by: Andrew Ammerlaan  gentoo.org>

 .../hdf5/files/hdf5-1.14.0-fix-include-path.patch  | 34 --
 1 file changed, 34 deletions(-)

diff --git a/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch 
b/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch
deleted file mode 100644
index 4530f1fa6d2e..
--- a/sci-libs/hdf5/files/hdf5-1.14.0-fix-include-path.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-https://bugs.gentoo.org/904515
-https://github.com/HDFGroup/hdf5/issues/2422
-https://github.com/HDFGroup/hdf5/issues/2621
-https://github.com/HDFGroup/hdf5/pull/2667
-https://github.com/HDFGroup/hdf5/commit/b77cb393b884c1dbdaffb300aa8c4967d9ba7fb0
-
-From b77cb393b884c1dbdaffb300aa8c4967d9ba7fb0 Mon Sep 17 00:00:00 2001
-From: jhendersonHDF 
-Date: Tue, 11 Apr 2023 14:31:25 -0500
-Subject: [PATCH] Fix improper include of build directory (#2422, #2621)
- (#2667)
-
 a/configure.ac
-+++ b/configure.ac
-@@ -3012,8 +3012,7 @@ SUBFILING_VFD=no
- HAVE_MERCURY="no"
- 
- ## Always include subfiling directory so public header files are available
--CPPFLAGS="$CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling"
--AM_CPPFLAGS="$AM_CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling"
-+H5_CPPFLAGS="$H5_CPPFLAGS -I$ac_abs_confdir/src/H5FDsubfiling"
- 
- AC_MSG_CHECKING([if the subfiling I/O virtual file driver (VFD) is enabled])
- 
-@@ -3061,8 +3060,7 @@ if test "X$SUBFILING_VFD" = "Xyes"; then
- mercury_dir="$ac_abs_confdir/src/H5FDsubfiling/mercury"
- mercury_inc="$mercury_dir/src/util"
- 
--CPPFLAGS="$CPPFLAGS -I$mercury_inc"
--AM_CPPFLAGS="$AM_CPPFLAGS -I$mercury_inc"
-+H5_CPPFLAGS="$H5_CPPFLAGS -I$mercury_inc"
- 
- HAVE_STDATOMIC_H="yes"
- AC_CHECK_HEADERS([stdatomic.h],,[HAVE_STDATOMIC_H="no"])

[gentoo-commits] repo/gentoo:master commit in: sci-libs/hdf5/files/, sci-libs/hdf5/

2023-04-13 Thread Sam James 
commit: 8763b1b03668dc7b0a681225b2013f216f4c
Author: Sam James  gentoo  org>
AuthorDate: Fri Apr 14 03:13:07 2023 +
Commit: Sam James  gentoo  org>
CommitDate: Fri Apr 14 03:23:03 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8763b1b0

sci-libs/hdf5: fix configure w/ clang 16

Signed-off-by: Sam James  gentoo.org>

 .../hdf5/files/hdf5-1.12.2-configure-clang16.patch | 30 ++
 ...hdf5-1.12.2-r5.ebuild => hdf5-1.12.2-r6.ebuild} |  1 +
 2 files changed, 31 insertions(+)

diff --git a/sci-libs/hdf5/files/hdf5-1.12.2-configure-clang16.patch 
b/sci-libs/hdf5/files/hdf5-1.12.2-configure-clang16.patch
new file mode 100644
index ..f341fa99ddac
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.12.2-configure-clang16.patch
@@ -0,0 +1,30 @@
+https://github.com/HDFGroup/hdf5/commit/9dd36f016a4316b94f5df15856d228de01d304c6
+
+From 9dd36f016a4316b94f5df15856d228de01d304c6 Mon Sep 17 00:00:00 2001
+From: Ryan Schmidt 
+Date: Thu, 17 Nov 2022 16:28:44 -0600
+Subject: [PATCH] Simplify & fix check for szlib encoder (#2263)
+
+Return the result rather than setting the exit code. "return" is a
+language keyword whereas "exit" is a function for which the 
+header has to be included which it wasn't in this test, therefore the
+test would previously fail to identify that the encoder was enabled if
+"-Werror=implicit-function-declaration" was used, which it is by default
+with clang from Xcode 12 and later.
+
+Fixes #2262
+--- a/configure.ac
 b/configure.ac
+@@ -1737,10 +1737,7 @@ if test "x$HAVE_SZLIB" = "xyes" -a "x$HAVE_SZLIB_H" = 
"xyes"; then
+ #include "szlib.h"
+ ],[[
+ /* SZ_encoder_enabled returns 1 if encoder is present */
+-if(SZ_encoder_enabled() == 1)
+-exit(0);
+-else
+-exit(1);
++return SZ_encoder_enabled() != 1;
+ ]])]
+ , [hdf5_cv_szlib_can_encode=yes], [hdf5_cv_szlib_can_encode=no],)]
+)
+

diff --git a/sci-libs/hdf5/hdf5-1.12.2-r5.ebuild 
b/sci-libs/hdf5/hdf5-1.12.2-r6.ebuild
similarity index 98%
rename from sci-libs/hdf5/hdf5-1.12.2-r5.ebuild
rename to sci-libs/hdf5/hdf5-1.12.2-r6.ebuild
index c27c86b3a6eb..c723c3ad3dde 100644
--- a/sci-libs/hdf5/hdf5-1.12.2-r5.ebuild
+++ b/sci-libs/hdf5/hdf5-1.12.2-r6.ebuild
@@ -38,6 +38,7 @@ PATCHES=(
"${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch
"${FILESDIR}"/${PN}-1.12.2-no-messing-ldpath.patch
"${FILESDIR}"/${PN}-1.12.2-no-strip-symbols.patch
+   "${FILESDIR}"/${PN}-1.12.2-configure-clang16.patch
 )
 
 pkg_setup() {

[gentoo-commits] repo/gentoo:master commit in: sci-libs/hdf5/files/

2022-05-02 Thread Sam James 
commit: 5dc5ca1f7ee5908d7d5e49814d154ce59848add9
Author: Sam James  gentoo  org>
AuthorDate: Tue May  3 02:35:26 2022 +
Commit: Sam James  gentoo  org>
CommitDate: Tue May  3 02:35:26 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5dc5ca1f

sci-libs/hdf5: add link to upstream PR for patch

Bug: https://github.com/HDFGroup/hdf5/pull/1716
Signed-off-by: Sam James  gentoo.org>

 sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch 
b/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch
index 8218f31aea66..6ea7520c0f13 100644
--- a/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch
+++ b/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch
@@ -1,3 +1,4 @@
+https://github.com/HDFGroup/hdf5/pull/1716
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
 @@ -46,6 +46,13 @@ if (CMAKE_VERSION VERSION_LESS "3.14.0")

[gentoo-commits] repo/gentoo:master commit in: sci-libs/hdf5/files/, sci-libs/hdf5/

2022-05-02 Thread Sam James 
commit: 9acdbbd4c8debd771ac4a6e39c1073551f7ce43f
Author: Sam James  gentoo  org>
AuthorDate: Tue May  3 02:27:07 2022 +
Commit: Sam James  gentoo  org>
CommitDate: Tue May  3 02:27:28 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9acdbbd4

sci-libs/hdf5: add 1.12.2

Lots of correctness and sanitizer fixes in .2 so possibly helps
with the sparc bug (although we've applied a workaround now anyway).

Bug: https://bugs.gentoo.org/686620
Signed-off-by: Sam James  gentoo.org>

 sci-libs/hdf5/Manifest |   1 +
 .../hdf5/files/hdf5-1.12.2-cmake_installdirs.patch | 163 +
 sci-libs/hdf5/hdf5-1.12.2.ebuild   | 119 +++
 3 files changed, 283 insertions(+)

diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index bd0243d24944..54270f9e0c89 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -1,2 +1,3 @@
 DIST hdf5-1.10.5.tar.bz2 8706317 BLAKE2B 
ac326be8fe4ccc4b0153f15bc7d65aa8f1adc2ae279d3980f57ed46722b754d3f36ecf1d6273c75e80ed1afd4bbf10c6b1c5d9408e1f83a4b2e397e7902a7d3c
 SHA512 
769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4
 DIST hdf5-1.12.1.tar.bz2 9724309 BLAKE2B 
cc75ba497188b33972218d02a7601acad1a0443bdb934ecd1641ef5996076fe120e3b72dba3a99d99f919fb4e478d1e531414448de9a7b97a0afde58a4c7c23f
 SHA512 
158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd
+DIST hdf5-1.12.2.tar.bz2 10494264 BLAKE2B 
99ca5b57f6f54fa044c909f0773de62b218c1f0ec3c011f88f3c227536dd719e77ddbe42d562b1214e8843e41d8fc56db499d7f122876fdd36ef31b235229cb7
 SHA512 
cbb4663570de76b11adb6bf62cfdb754371d31eeab04691479a5764a45207a9c1309665ab80f51c63a4b9b87354f9cbe6835cef506a9fd554d142c6d2bec21e5

diff --git a/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch 
b/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch
new file mode 100644
index ..8218f31aea66
--- /dev/null
+++ b/sci-libs/hdf5/files/hdf5-1.12.2-cmake_installdirs.patch
@@ -0,0 +1,163 @@
+--- a/CMakeLists.txt
 b/CMakeLists.txt
+@@ -46,6 +46,13 @@ if (CMAKE_VERSION VERSION_LESS "3.14.0")
+   endif()
+ endif ()
+ 
++include (GNUInstallDirs)
++set (HDF5_INSTALL_BIN_DIR "${CMAKE_INSTALL_FULL_BINDIR}")
++set (HDF5_INSTALL_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}")
++set (HDF5_INSTALL_DOC_DIR "${CMAKE_INSTALL_FULL_DOCDIR}")
++set (HDF5_INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_FULL_INCLUDEDIR}")
++set (HDF5_INSTALL_LIB_DIR "${CMAKE_INSTALL_FULL_LIBDIR}")
++
+ #-
+ # Instructions for use : Sub-Project Build
+ #
+--- a/c++/src/CMakeLists.txt
 b/c++/src/CMakeLists.txt
+@@ -173,8 +173,8 @@ endif ()
+ #-
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_CPP_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+--- a/doxygen/CMakeLists.txt
 b/doxygen/CMakeLists.txt
+@@ -36,7 +36,7 @@ if (DOXYGEN_FOUND)
+ 
+   install (
+   DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html
+-  DESTINATION ${HDF5_INSTALL_DATA_DIR}
++  DESTINATION ${HDF5_INSTALL_DOC_DIR}
+   COMPONENT Documents
+   )
+ 
+--- a/fortran/src/CMakeLists.txt
 b/fortran/src/CMakeLists.txt
+@@ -537,8 +537,8 @@ endif ()
+ #-
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_F90_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+--- a/hl/c++/src/CMakeLists.txt
 b/hl/c++/src/CMakeLists.txt
+@@ -91,8 +91,8 @@ endif ()
+ #-
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
++set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
++set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_HL_CPP_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+--- a/hl/fortran/src/CMakeLists.txt
 b/hl/fortran/src/CMakeLists.txt
+@@ -324,8 +324,8 @@

[gentoo-commits] repo/gentoo:master commit in: sci-libs/hdf5/files/, sci-libs/hdf5/

2019-06-15 Thread Andreas Sturmlechner 
commit: df2c62a10c80eb73d5c12bf143ae1c2c2321d980
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sat Jun 15 19:42:00 2019 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sat Jun 15 20:56:08 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=df2c62a1

sci-libs/hdf5: Drop 1.8.18 and 1.10.1

Package-Manager: Portage-2.3.67, Repoman-2.3.14
Signed-off-by: Andreas Sturmlechner  gentoo.org>

 sci-libs/hdf5/Manifest  |   2 -
 sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch |  43 -
 sci-libs/hdf5/hdf5-1.10.1.ebuild|  95 
 sci-libs/hdf5/hdf5-1.8.18.ebuild| 111 
 sci-libs/hdf5/metadata.xml  |   5 +-
 5 files changed, 1 insertion(+), 255 deletions(-)

diff --git a/sci-libs/hdf5/Manifest b/sci-libs/hdf5/Manifest
index e8b5dd2438c..64df5831a55 100644
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@@ -1,3 +1 @@
-DIST hdf5-1.10.1.tar.bz2 11769617 BLAKE2B 
66ad762aed90cea9e58a9735bf0e189d78befc40cac0e566586e967f2b3ba6f5bf8a6bfd12a2f4062f8b20900c16d467c34134c17dedfd8f345cb96bd853a2fe
 SHA512 
266b0e2f28c5fd540099a4955244ddb8c03aca3ad40d626358643f033a6ae5e9266a1d6c1d60925c7d42d24d28a1549d3305fe8ddb42cec2379af7231b93e554
 DIST hdf5-1.10.5.tar.bz2 8706317 BLAKE2B 
ac326be8fe4ccc4b0153f15bc7d65aa8f1adc2ae279d3980f57ed46722b754d3f36ecf1d6273c75e80ed1afd4bbf10c6b1c5d9408e1f83a4b2e397e7902a7d3c
 SHA512 
769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4
-DIST hdf5-1.8.18.tar.bz2 10081294 BLAKE2B 
cf0d0c8a41576bcf816460eaabcfab29cfffba240721a64fe584c42fbb322470f29fb93c8513f7bbdedeeb392c2fe64cd3261b47b47de5b01828dae0b1929cd3
 SHA512 
01f6d14bdd3be2ced9c63cc9e1820cd7ea11db649ff9f3a3055c18c4b0fffe777fd23baad536e3bce31c4d76fe17db64a3972762e1bb4d232927c1ca140e72b2

diff --git a/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch 
b/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch
deleted file mode 100644
index 72e09617097..000
--- a/sci-libs/hdf5/files/hdf5-1.8.15-implicits.patch
+++ /dev/null
@@ -1,43 +0,0 @@
 a/hl/src/H5LTanalyze.c
-+++ b/hl/src/H5LTanalyze.c
-@@ -40,6 +40,7 @@
- #include 
- #include 
- #include 
-+#include 
- 
- /* end standard C headers. */
- 
 a/hl/src/H5LTanalyze.l
-+++ b/hl/src/H5LTanalyze.l
-@@ -16,6 +16,7 @@
- %{
- #include 
- #include 
-+#include 
- #include 
- #include "H5LTparse.h"
- 
 a/test/cache_common.h
-+++ b/test/cache_common.h
-@@ -702,5 +702,8 @@ void validate_mdc_config(hid_t file_id,
-  hbool_t compare_init,
-  int test_num);
- 
-+hbool_t resize_configs_are_equal(const H5C_auto_size_ctl_t *a,
-+ const H5C_auto_size_ctl_t *b,
-+ hbool_t compare_init);
- #endif /* _CACHE_COMMON_H */
- 
 a/testpar/t_span_tree.c
-+++ b/testpar/t_span_tree.c
-@@ -37,6 +37,9 @@
- #include "hdf5.h"
- #include "H5private.h"
- #include "testphdf5.h"
-+#define H5S_PACKAGE
-+#define H5S_TESTING
-+#include "H5Spkg.h"
- 
- 
- static void coll_write_test(int chunk_factor);

diff --git a/sci-libs/hdf5/hdf5-1.10.1.ebuild b/sci-libs/hdf5/hdf5-1.10.1.ebuild
deleted file mode 100644
index 6cf18a83be0..000
--- a/sci-libs/hdf5/hdf5-1.10.1.ebuild
+++ /dev/null
@@ -1,95 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-FORTRAN_NEEDED=fortran
-AUTOTOOLS_AUTORECONF=1
-
-inherit autotools-utils eutils fortran-2 flag-o-matic toolchain-funcs multilib 
versionator prefix
-
-MY_P=${PN}-${PV/_p/-patch}
-MAJOR_P=${PN}-$(get_version_component_range 1-2 ${PV})
-
-DESCRIPTION="General purpose library and file format for storing scientific 
data"
-HOMEPAGE="http://www.hdfgroup.org/HDF5/;
-SRC_URI="http://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2;
-
-LICENSE="NCSA-HDF"
-SLOT="0/${PV%%_p*}"
-KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd 
~amd64-linux ~x86-linux"
-IUSE="cxx debug examples fortran +hl mpi static-libs szip threads zlib"
-
-REQUIRED_USE="
-   cxx? ( !mpi ) mpi? ( !cxx )
-   threads? ( !cxx !mpi !fortran !hl )"
-
-RDEPEND="
-   mpi? ( virtual/mpi[romio] )
-   szip? ( virtual/szip )
-   zlib? ( sys-libs/zlib:0= )"
-
-DEPEND="${RDEPEND}
-   sys-devel/libtool:2
-   >=sys-devel/autoconf-2.69"
-
-S="${WORKDIR}/${MY_P}"
-
-PATCHES=(
-   "${FILESDIR}"/${PN}-1.8.9-static_libgfortran.patch
-   "${FILESDIR}"/${PN}-1.8.9-mpicxx.patch
-   "${FILESDIR}"/${PN}-1.8.13-no-messing-ldpath.patch
-)
-
-pkg_setup() {
-   tc-export CXX CC AR # workaround for bug 285148
-   use fortran && fortran-2_pkg_setup
-
-   if use mpi; then
-   if has_version 'sci-libs/hdf5[-mpi]'; then
-   ewarn "Installing hdf5 with mpi enabled with a previous