[gentoo-commits] repo/gentoo:master commit in: sci-libs/silo/, sci-libs/silo/files/
commit: 563f6de9fc73190ad10ae3778fe3ede11a42f7e3
Author: Sam James gentoo org>
AuthorDate: Sun Mar 17 07:48:42 2024 +
Commit: Sam James gentoo org>
CommitDate: Sun Mar 17 07:49:44 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=563f6de9
sci-libs/silo: add 4.11.1
* Partially fix tests with GCC 14 (reported another issue on the upstream PR
for that).
* Disable LTO and SA given the comments on a linked upstream bug wrt
opimisation.
Closes: https://bugs.gentoo.org/862927
Signed-off-by: Sam James gentoo.org>
sci-libs/silo/Manifest| 1 +
sci-libs/silo/files/silo-4.11.1-gcc14-tests.patch | 45
sci-libs/silo/silo-4.11.1.ebuild | 63 +++
3 files changed, 109 insertions(+)
diff --git a/sci-libs/silo/Manifest b/sci-libs/silo/Manifest
index f860b2cafed1..a2470626ee06 100644
--- a/sci-libs/silo/Manifest
+++ b/sci-libs/silo/Manifest
@@ -1 +1,2 @@
DIST silo-4.11-bsd.tgz 13298515 BLAKE2B
fcf2e7912381e57d1a64644d3cee4dea50302c12704eaf0ee9e2569b7bc29b1d5c9df66878744ffc2cc04e16834fdf1cd4d677983af36005e4ecf0918c6283d5
SHA512
f642dd21dacffa147aea54d6f8669c704772d5640d6eb7eeff1d7e5e5d37ddbde250d78bad30e9478dcfec63a86863243d7a56cd9b692eaefdd7a89b34df35d0
+DIST silo-4.11.1-bsd.tar.xz 4581480 BLAKE2B
577bb9e367cae08496ec2062ce7b1fc6ebd04a8221bfb304585ea8b338502793a8ba43c14dbf8a7fd1f61b3c8a3a7886da1e9a7f9a1972d2a9cb69d5e36362e3
SHA512
e4ecfc434b43ea0bd2e3cda469f5e232b0bdfd25a44da04e77f2213ff20fd4158bc085d16b10de22d9a4be0ce822899e2b7f20c53b4d4bd941f92357a873c4a2
diff --git a/sci-libs/silo/files/silo-4.11.1-gcc14-tests.patch
b/sci-libs/silo/files/silo-4.11.1-gcc14-tests.patch
new file mode 100644
index ..1e729ee74e32
--- /dev/null
+++ b/sci-libs/silo/files/silo-4.11.1-gcc14-tests.patch
@@ -0,0 +1,45 @@
+https://github.com/LLNL/Silo/pull/371
+
+From f0737787eb02093defc30de05a731ffe63c4c6f4 Mon Sep 17 00:00:00 2001
+From: Sam James
+Date: Sun, 17 Mar 2024 07:35:36 +
+Subject: [PATCH] tests: add missing header for `difftime`
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+With GCC 14, which makes implicit function declarations an error by default:
+```
+TestReadMask.c: In function ‘ElapsedTime’:
+TestReadMask.c:746:15: error: implicit declaration of function ‘difftime’
[-Wimplicit-function-declaration]
+ 746 | ms = (int)difftime(end_time.tv_sec, start_time.tv_sec);
+ | ^~~~
+TestReadMask.c:62:1: note: ‘difftime’ is defined in header ‘’; this is
probably fixable by adding ‘#include ’
+ 61 | #include
+ +++ |+#include
+ 62 |
+```
+
+Fix the include guards and include unconditionally (for difftime) and
+unconditionally too (for memcpy).
+
+Signed-off-by: Sam James
+--- a/tests/TestReadMask.c
b/tests/TestReadMask.c
+@@ -51,13 +51,12 @@ product endorsement purposes.
+ */
+ #include
+ #include
++#include
+ #ifndef WIN32
+ #include
+-#else
+-#include
+-#include
+ #endif
+ #include
++#include
+ #include
+
+ /* To compile this program on hyper, here is the command:
+
diff --git a/sci-libs/silo/silo-4.11.1.ebuild b/sci-libs/silo/silo-4.11.1.ebuild
new file mode 100644
index ..78b80eb13d33
--- /dev/null
+++ b/sci-libs/silo/silo-4.11.1.ebuild
@@ -0,0 +1,63 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic fortran-2 qmake-utils
+
+DESCRIPTION="A mesh and field I/O library and scientific database"
+HOMEPAGE="https://software.llnl.gov/Silo/;
+SRC_URI="https://github.com/LLNL/Silo/releases/download/${PV}/${P}-bsd.tar.xz;
+S="${WORKDIR}/${P}-bsd"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="browser +hdf5 +silex"
+
+# see bugs 656432 and 741741
+RDEPEND="
+ dev-qt/qtcore:5
+ dev-qt/qtgui:5
+ dev-qt/qtwidgets:5
+ net-dialup/lrzsz
+ virtual/szip
+ hdf5? ( sci-libs/hdf5 )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="dev-qt/linguist-tools:5"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-4.11-test-disable-largefile.patch
+ "${FILESDIR}"/${PN}-4.11-tests.patch
+ "${FILESDIR}"/${PN}-4.11-testsuite-python-write.patch
+ "${FILESDIR}"/${PN}-4.11-widgets.patch
+ "${FILESDIR}"/${PN}-4.11-qtbindir.patch
+ "${FILESDIR}"/${PN}-4.11.1-gcc14-tests.patch
+)
+
+src_configure() {
+ # bug #862927 and https://github.com/LLNL/Silo/issues/248
+ append-flags -fno-strict-aliasing
+ filter-lto
+
+ # add fflags for fixing test bug on matf77.f
+ # see https://github.com/LLNL/Silo/issues/234
+ append-fflags $(test-flags-F77 -fallow-argument-mismatch)
+
+ CONFIG_SHELL="${BROOT}"/bin/bash \
+ QMAKE=$(qt5_get_bindir)/qmake \
+ QT_BIN_DIR=$(qt5_get_bindir) \
+ econf \
+ --enable-install-lite-headers \
+ --enable-shared \
+ $(use_enable silex silex ) \
+
[gentoo-commits] repo/gentoo:master commit in: sci-libs/silo/, sci-libs/silo/files/
commit: b7fbed581008c7f7e6c6e16028341b60862cd002
Author: Marco Scardovi scardovi com>
AuthorDate: Tue Dec 14 22:01:46 2021 +
Commit: Jakov Smolić gentoo org>
CommitDate: Wed Jan 5 19:51:33 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b7fbed58
sci-libs/silo: bump to 4.11 and EAPI 8
I have restricted test because it's broken right now in 4.11
(there's a problem about mismatch in a fortran file, matf77.f).
Following the archlinux way I've moved to the BSD version in
order to use only BSD license (the full version requires some
non-free licenses and We don't really need to complain against them).
This PR also bump to latest EAPI (see bug below)
and add USE flag browser for browser support
Closes: https://bugs.gentoo.org/828693
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Marco Scardovi scardovi.com>
Signed-off-by: Jakov Smolić gentoo.org>
sci-libs/silo/Manifest | 1 +
sci-libs/silo/files/silo-4.10.2-mpiposix.patch | 53 ---
sci-libs/silo/files/silo-4.10.2-qt5.patch | 44
sci-libs/silo/files/silo-4.10.2-qtlibs.patch | 78 --
sci-libs/silo/files/silo-4.10.2-tests.patch| 11 ---
sci-libs/silo/files/silo-4.11-autoreconf.patch | 35 ++
sci-libs/silo/files/silo-4.11-hdf5.patch | 46 +
.../files/silo-4.11-test-disable-largefile.patch | 23 +++
sci-libs/silo/files/silo-4.11-tests.patch | 26
.../files/silo-4.11-testsuite-python-write.patch | 27
sci-libs/silo/metadata.xml | 1 +
sci-libs/silo/silo-4.11.ebuild | 47 +
12 files changed, 206 insertions(+), 186 deletions(-)
diff --git a/sci-libs/silo/Manifest b/sci-libs/silo/Manifest
index b6f65c970d1f..c2c68f4d8730 100644
--- a/sci-libs/silo/Manifest
+++ b/sci-libs/silo/Manifest
@@ -1 +1,2 @@
DIST silo-4.10.2.tar.gz 13135900 BLAKE2B
6326a42df43c4bb6936522d1730db8ce45c6b74779cf37b7a5a0b7a72def9e9a4f174b68392adbda59936113ccac4ae5e7bf7266effb364eac7e5d0cff8bb37c
SHA512
8cd1340ed641c8be77f310b286da344e2fed7ae469ed7bebf5deebaa1a369ca91c283b38eae2c57b7ad046f65343cfaa56a1c07b6c8b07b79aad69c4e5617f6e
+DIST silo-4.11-bsd.tgz 13298515 BLAKE2B
fcf2e7912381e57d1a64644d3cee4dea50302c12704eaf0ee9e2569b7bc29b1d5c9df66878744ffc2cc04e16834fdf1cd4d677983af36005e4ecf0918c6283d5
SHA512
f642dd21dacffa147aea54d6f8669c704772d5640d6eb7eeff1d7e5e5d37ddbde250d78bad30e9478dcfec63a86863243d7a56cd9b692eaefdd7a89b34df35d0
diff --git a/sci-libs/silo/files/silo-4.10.2-mpiposix.patch
b/sci-libs/silo/files/silo-4.10.2-mpiposix.patch
deleted file mode 100644
index 30a3f910b196..
--- a/sci-libs/silo/files/silo-4.10.2-mpiposix.patch
+++ /dev/null
@@ -1,53 +0,0 @@
src/hdf5_drv/silo_hdf5.c.orig 2017-07-28 08:52:09.026638768 +0200
-+++ src/hdf5_drv/silo_hdf5.c 2017-07-28 09:00:12.306635882 +0200
-@@ -4752,18 +4752,19 @@
- }
-
- /* default HDF5 mpi drivers */
--case DB_FILE_OPTS_H5_DEFAULT_MPIP:
--{
--#ifdef H5_HAVE_PARALLEL
--h5status |= H5Pset_fapl_mpiposix(retval, MPI_COMM_SELF, TRUE);
--#else
--H5Pclose(retval);
--return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
--#endif
--break;
--}
-+//case DB_FILE_OPTS_H5_DEFAULT_MPIP:
-+//{
-+//#ifdef H5_HAVE_PARALLEL
-+//h5status |= H5Pset_fapl_mpiposix(retval, MPI_COMM_SELF, TRUE);
-+//#else
-+//H5Pclose(retval);
-+//return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
-+//#endif
-+//break;
-+//}
-
- case DB_FILE_OPTS_H5_DEFAULT_MPIO:
-+ case DB_FILE_OPTS_H5_DEFAULT_MPIP:
- {
- #ifdef H5_HAVE_PARALLEL
- MPI_Info info;
-@@ -5069,15 +5070,15 @@
- if ((p = DBGetOption(opts, DBOPT_H5_MPIP_NO_GPFS_HINTS)))
- use_gpfs_hints = FALSE;
-
--if (vfd == DB_H5VFD_MPIO)
-+//if (vfd == DB_H5VFD_MPIO)
- {
- h5status |= H5Pset_fapl_mpio(retval, mpi_comm,
mpi_info);
- if (created_info) MPI_Info_free(_info);
- }
--else
--{
--h5status |= H5Pset_fapl_mpiposix(retval, mpi_comm,
use_gpfs_hints);
--}
-+//else
-+//{
-+//h5status |= H5Pset_fapl_mpiposix(retval, mpi_comm,
use_gpfs_hints);
-+//}
- #else
- H5Pclose(retval);
- return db_perror("HDF5 MPI VFD", E_NOTENABLEDINBUILD, me);
diff --git a/sci-libs/silo/files/silo-4.10.2-qt5.patch
b/sci-libs/silo/files/silo-4.10.2-qt5.patch
deleted file mode 100644
index 1e1fe8803a37..
---
