* [gentoo-commits] repo/gentoo:master commit in: sci-libs/netcdf/files/, sci-libs/netcdf/
@ 2022-07-15 12:49 Sam James
0 siblings, 0 replies; 3+ messages in thread
From: Sam James @ 2022-07-15 12:49 UTC (permalink / raw
To: gentoo-commits
commit: 400a204bea4aa72d51a0ef53260743c9f7ee0310
Author: brahmajit das <brahmajit.xyz <AT> gmail <DOT> com>
AuthorDate: Fri Jul 15 10:13:20 2022 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Fri Jul 15 12:46:42 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=400a204b
sci-libs/netcdf: Fix musl missing execinfo.h check
Check if execinfo.h is present before including the header. The check is
preset in other parts of the souce code, here it was only being checked if
it's WIN32 or CYGIWIN before including execinfo.h as a result build was
failing on musl.
Closes: https://bugs.gentoo.org/828677
Signed-off-by: brahmajit das <brahmajit.xyz <AT> gmail.com>
Closes: https://github.com/gentoo/gentoo/pull/26284
Signed-off-by: Sam James <sam <AT> gentoo.org>
.../files/netcdf-4.9.0-fix-musl-execinfo_h.patch | 46 ++++++++++++++++++++++
sci-libs/netcdf/netcdf-4.9.0.ebuild | 1 +
2 files changed, 47 insertions(+)
diff --git a/sci-libs/netcdf/files/netcdf-4.9.0-fix-musl-execinfo_h.patch b/sci-libs/netcdf/files/netcdf-4.9.0-fix-musl-execinfo_h.patch
new file mode 100644
index 000000000000..7b711327512a
--- /dev/null
+++ b/sci-libs/netcdf/files/netcdf-4.9.0-fix-musl-execinfo_h.patch
@@ -0,0 +1,46 @@
+# Conditionally include execinfo as it's not available on all libc
+# systems. There is a PR upstream for a similiar issue but the actual
+# issus is not reproducable on Gentoo [math library not found] [1], so
+# for now this is a temporary fix and can be removed once the PR [1]
+# is merged upstream.
+# [1]: https://github.com/Unidata/netcdf-c/pull/1701
+#
+# Closes: https://bugs.gentoo.org/828677
+--- a/libhdf5/hdf5debug.c
++++ b/libhdf5/hdf5debug.c
+@@ -5,7 +5,7 @@
+ #include "config.h"
+ #include <stdarg.h>
+ #include <stdio.h>
+-#if !defined _WIN32 && !defined __CYGWIN__
++#ifdef HAVE_EXECINFO_H
+ #include <execinfo.h>
+ #endif
+
+@@ -15,15 +15,18 @@
+
+ #define STSIZE 1000
+
++#ifdef HAVE_EXECINFO_H
+ #ifdef H5BACKTRACE
+ # if !defined _WIN32 && !defined __CYGWIN__
+ static void* stacktrace[STSIZE];
+ # endif
+ #endif
++#endif
+
+ int
+ nch5breakpoint(int err)
+ {
++#ifdef HAVE_EXECINFO_H
+ #ifdef H5BACKTRACE
+ # if !defined _WIN32 && !defined __CYGWIN__
+ int count = 0;
+@@ -39,6 +42,7 @@ nch5breakpoint(int err)
+ if(trace != NULL) free(trace);
+ # endif
+ # endif
++#endif
+ #endif
+ return err;
+ }
diff --git a/sci-libs/netcdf/netcdf-4.9.0.ebuild b/sci-libs/netcdf/netcdf-4.9.0.ebuild
index 8ffc629f18a2..651ca0381223 100644
--- a/sci-libs/netcdf/netcdf-4.9.0.ebuild
+++ b/sci-libs/netcdf/netcdf-4.9.0.ebuild
@@ -36,6 +36,7 @@ REQUIRED_USE="
PATCHES=(
"${FILESDIR}"/${PN}-4.7.4-big-endian-test.patch
+ "${FILESDIR}"/${PN}-4.9.0-fix-musl-execinfo_h.patch
)
src_configure() {
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-libs/netcdf/files/, sci-libs/netcdf/
@ 2022-12-19 14:47 Andreas Sturmlechner
0 siblings, 0 replies; 3+ messages in thread
From: Andreas Sturmlechner @ 2022-12-19 14:47 UTC (permalink / raw
To: gentoo-commits
commit: 0385f93e6025666a54f61333fe1cda1d846b830d
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 18 11:32:14 2022 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Mon Dec 19 14:44:55 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0385f93e
sci-libs/netcdf: drop 4.7.4
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
sci-libs/netcdf/Manifest | 1 -
.../files/netcdf-4.7.4-big-endian-build.patch | 63 ------------------
sci-libs/netcdf/netcdf-4.7.4.ebuild | 74 ----------------------
3 files changed, 138 deletions(-)
diff --git a/sci-libs/netcdf/Manifest b/sci-libs/netcdf/Manifest
index 846d67b85759..462625e792e9 100644
--- a/sci-libs/netcdf/Manifest
+++ b/sci-libs/netcdf/Manifest
@@ -1,3 +1,2 @@
-DIST netcdf-4.7.4.tar.gz 19711158 BLAKE2B b49532e6f87b458e7f5654f70ec932d6c8c81272c97ce44df3d27bb61b01d3e005f918b959ce12e42e26f7c12309ab72eeb57a35216d20ab5761837db65741a4 SHA512 15922818fdd71be285eb7dd2fc9be2594fe9af979de3ed316465636c7bbdaec65eb151ca57ef8b703e6a360cdba036b8f9bc193ddff01ff7ce4214c0a66efa79
DIST netcdf-4.8.1.tar.gz 18957280 BLAKE2B 05fc6cd10cb5cbb11dc077b9a884fbc63c4cb840b241e782702da58ad9831fba065a6f1e97c2be092437735d39658482285850a00618d0582d6e4728d64c4402 SHA512 c97207867abf10d414abf34624268710f5b812c26c38f97e73afe00558b3f07917331fbc7fdb9e70b09813acf15a9a09bae2c432a3266ce10a791b9472f87a42
DIST netcdf-4.9.0.tar.gz 19491744 BLAKE2B b669f7ccb2f7a8def9d5b944a97d101ea7b7307d6e1495a97c0966b4ac9722b404d6039dee192da759d14d52259be2ff4f49be3bfb6cbbfac48732684cbff9c3 SHA512 62cb593b99a6e9c56426175d141907572d3974de8dc39549c85337acf410539f9b7dcd9a375808e271da1d0dc93fce7586b955eddd2bb45901d9cc48a72db705
diff --git a/sci-libs/netcdf/files/netcdf-4.7.4-big-endian-build.patch b/sci-libs/netcdf/files/netcdf-4.7.4-big-endian-build.patch
deleted file mode 100644
index edad05a21e64..000000000000
--- a/sci-libs/netcdf/files/netcdf-4.7.4-big-endian-build.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-https://github.com/DennisHeimbigner/netcdf-c/commit/6f86660da86f279cad1f2804cf3242767de27630.patch
-https://github.com/Unidata/netcdf-c/issues/1687
-https://bugs.gentoo.org/772863
-
-From 6f86660da86f279cad1f2804cf3242767de27630 Mon Sep 17 00:00:00 2001
-From: Dennis Heimbigner <dmh@ucar.edu>
-Date: Fri, 3 Apr 2020 20:15:34 -0600
-Subject: [PATCH] Fix missing forward declarations
-
-re: issue https://github.com/Unidata/netcdf-c/issues/1687
-
-static functions are being used before decl and it causes
-errors. Only occurs when BIG_ENDIAN is defined.
-Solution is to add the forward declarations.
----
- libdispatch/dfilter.c | 4 ++++
- nc_test4/tst_filterparser.c | 5 +++++
- plugins/H5Zutil.c | 1 +
- 3 files changed, 10 insertions(+)
-
-diff --git a/libdispatch/dfilter.c b/libdispatch/dfilter.c
-index 893846457..0e490a3d6 100644
---- a/libdispatch/dfilter.c
-+++ b/libdispatch/dfilter.c
-@@ -40,6 +40,10 @@ Unified filter related code
-
- /* Forward */
- static int gettype(const int q0, const int q1, int* unsignedp);
-+#ifdef WORDS_BIGENDIAN
-+static void byteswap8(unsigned char* mem);
-+static void byteswap4(unsigned char* mem);
-+#endif
-
- const struct LegalFormat {
- const char* tag;
-diff --git a/nc_test4/tst_filterparser.c b/nc_test4/tst_filterparser.c
-index 7d02f2bc7..b32094a25 100644
---- a/nc_test4/tst_filterparser.c
-+++ b/nc_test4/tst_filterparser.c
-@@ -122,6 +122,11 @@ static const char* spectype[] = {"i", "b", "ub", "s", "us", "i", "ui", "i", "i",
-
- static int nerrs = 0;
-
-+#ifdef WORDS_BIGENDIAN
-+static void byteswap8(unsigned char* mem);
-+static void byteswap4(unsigned char* mem);
-+#endif
-+
- static void
- mismatch(size_t i, unsigned int *params, const char* tag)
- {
-diff --git a/plugins/H5Zutil.c b/plugins/H5Zutil.c
-index cb36dc96c..86dfb0cfa 100644
---- a/plugins/H5Zutil.c
-+++ b/plugins/H5Zutil.c
-@@ -4,6 +4,7 @@
- */
-
-
-+#include "config.h"
- #include <hdf5.h>
-
- /*
diff --git a/sci-libs/netcdf/netcdf-4.7.4.ebuild b/sci-libs/netcdf/netcdf-4.7.4.ebuild
deleted file mode 100644
index 793ea43ad586..000000000000
--- a/sci-libs/netcdf/netcdf-4.7.4.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake flag-o-matic
-
-DESCRIPTION="Scientific library and interface for array oriented data access"
-HOMEPAGE="https://www.unidata.ucar.edu/software/netcdf/"
-SRC_URI="https://github.com/Unidata/netcdf-c/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}-c-${PV}"
-
-LICENSE="UCAR-Unidata"
-SLOT="0/18"
-KEYWORDS="amd64 ~arm ~arm64 ~ia64 ppc ppc64 -riscv x86 ~amd64-linux ~x86-linux"
-IUSE="+dap doc examples hdf +hdf5 mpi szip test tools"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dap? ( net-misc/curl:0= )
- hdf? (
- sci-libs/hdf:0=
- sci-libs/hdf5:0=
- virtual/jpeg
- )
- hdf5? ( sci-libs/hdf5:0=[hl(+),mpi=,szip=,zlib] )"
-DEPEND="${RDEPEND}"
-BDEPEND="
- doc? ( app-doc/doxygen[dot] )
- virtual/pkgconfig"
-
-REQUIRED_USE="
- test? ( tools )
- szip? ( hdf5 )
- mpi? ( hdf5 )"
-
-PATCHES=(
- "${FILESDIR}/${PN}-4.7.4-big-endian-build.patch"
- "${FILESDIR}/${PN}-4.7.4-big-endian-test.patch"
-)
-
-src_prepare() {
- # skip test that requires network
- sed -i -e '/run_get_hdf4_files/d' hdf4_test/CMakeLists.txt || die
-
- cmake_src_prepare
-}
-
-src_configure() {
- use mpi && export CC=mpicc
-
- # Temporary workaround for test breakage
- # https://github.com/Unidata/netcdf-c/issues/1983
- # bug #827042
- append-flags -fno-strict-aliasing
-
- local mycmakeargs=(
- -DENABLE_DAP_REMOTE_TESTS=OFF
- -DBUILD_UTILITIES=$(usex tools)
- -DENABLE_DAP=$(usex dap)
- -DENABLE_DOXYGEN=$(usex doc)
- -DENABLE_EXAMPLES=$(usex examples)
- -DENABLE_HDF4=$(usex hdf)
- -DENABLE_NETCDF_4=$(usex hdf5)
- -DENABLE_TESTS=$(usex test)
- )
-
- cmake_src_configure
-}
-
-src_test() {
- # fails parallel tests: bug #621486
- cmake_src_test -j1
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread* [gentoo-commits] repo/gentoo:master commit in: sci-libs/netcdf/files/, sci-libs/netcdf/
@ 2023-07-27 19:42 Andreas Sturmlechner
0 siblings, 0 replies; 3+ messages in thread
From: Andreas Sturmlechner @ 2023-07-27 19:42 UTC (permalink / raw
To: gentoo-commits
commit: 870f87cd80955a072eaa313b22bb7447f2dd8967
Author: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
AuthorDate: Thu Jul 27 18:27:51 2023 +0000
Commit: Andreas Sturmlechner <asturm <AT> gentoo <DOT> org>
CommitDate: Thu Jul 27 19:42:39 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=870f87cd
sci-libs/netcdf: drop 4.8.1-r1, 4.8.1-r2
Closes: https://bugs.gentoo.org/886889
Signed-off-by: Andreas Sturmlechner <asturm <AT> gentoo.org>
sci-libs/netcdf/Manifest | 1 -
.../files/netcdf-4.8.1-big-endian-build.patch | 24 -------
sci-libs/netcdf/metadata.xml | 1 -
sci-libs/netcdf/netcdf-4.8.1-r1.ebuild | 76 --------------------
sci-libs/netcdf/netcdf-4.8.1-r2.ebuild | 83 ----------------------
5 files changed, 185 deletions(-)
diff --git a/sci-libs/netcdf/Manifest b/sci-libs/netcdf/Manifest
index c6c25e69d50e..bae5000b682d 100644
--- a/sci-libs/netcdf/Manifest
+++ b/sci-libs/netcdf/Manifest
@@ -1,2 +1 @@
-DIST netcdf-4.8.1.tar.gz 18957280 BLAKE2B 05fc6cd10cb5cbb11dc077b9a884fbc63c4cb840b241e782702da58ad9831fba065a6f1e97c2be092437735d39658482285850a00618d0582d6e4728d64c4402 SHA512 c97207867abf10d414abf34624268710f5b812c26c38f97e73afe00558b3f07917331fbc7fdb9e70b09813acf15a9a09bae2c432a3266ce10a791b9472f87a42
DIST netcdf-c-4.9.2.tar.gz 7142536 BLAKE2B b24135070d2f1f0b53fe738f8839039547eceba16d36905bb8cd7be983ce0c1127b7b01ae37dbde50087aa82fd56f00fab9bfa75c7d94fd4478031bb8a6da247 SHA512 7a96bcf673d5a9e1537d660aaf085a1dfaefc7dfb0fc96358462d92e7bbfe541184583681797e6a54d11b8588504b7d8a9b0b9bd850eecd02ed73aa2eb5ffa0d
diff --git a/sci-libs/netcdf/files/netcdf-4.8.1-big-endian-build.patch b/sci-libs/netcdf/files/netcdf-4.8.1-big-endian-build.patch
deleted file mode 100644
index afeff7e3fbd0..000000000000
--- a/sci-libs/netcdf/files/netcdf-4.8.1-big-endian-build.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Later version for 4.8.1 grabbed from Debian:
-https://sources.debian.org/patches/netcdf/1:4.8.1-1/byteswap.patch/
-
-Earlier version used:
-https://github.com/DennisHeimbigner/netcdf-c/commit/6f86660da86f279cad1f2804cf3242767de27630.patch
-https://github.com/Unidata/netcdf-c/issues/1687
-https://bugs.gentoo.org/772863
-
-Description: Add forward declarations for byteswap8 & byteswap4.
-Author: Dennis Heimbigner
-Bug: https://github.com/Unidata/netcdf-c/issues/1687
-
---- a/libdispatch/dfilter.c
-+++ b/libdispatch/dfilter.c
-@@ -20,6 +20,9 @@
- #include "hdf5internal.h"
- #endif
-
-+static void byteswap8(unsigned char*);
-+static void byteswap4(unsigned char*);
-+
- /*
- Unified filter related code
- */
diff --git a/sci-libs/netcdf/metadata.xml b/sci-libs/netcdf/metadata.xml
index acecc3ab2966..710afdc8ff08 100644
--- a/sci-libs/netcdf/metadata.xml
+++ b/sci-libs/netcdf/metadata.xml
@@ -16,7 +16,6 @@
<use>
<flag name="dap">Support for remote data access with the built-in OPeNDAP client</flag>
<flag name="hdf">Add support for the Hierarchical Data Format v.4 <pkg>sci-libs/hdf</pkg></flag>
- <flag name="tools">Build the utilities nccopy, ncgen and ncdump</flag>
</use>
<upstream>
<remote-id type="github">Unidata/netcdf-c</remote-id>
diff --git a/sci-libs/netcdf/netcdf-4.8.1-r1.ebuild b/sci-libs/netcdf/netcdf-4.8.1-r1.ebuild
deleted file mode 100644
index 003e1303571f..000000000000
--- a/sci-libs/netcdf/netcdf-4.8.1-r1.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake flag-o-matic
-
-DESCRIPTION="Scientific library and interface for array oriented data access"
-HOMEPAGE="https://www.unidata.ucar.edu/software/netcdf/"
-SRC_URI="https://github.com/Unidata/netcdf-c/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}-c-${PV}"
-
-LICENSE="UCAR-Unidata"
-# SONAME of libnetcdf.so
-SLOT="0/19"
-KEYWORDS="amd64 ~arm ~arm64 ~ia64 ~ppc ppc64 -riscv ~x86 ~amd64-linux ~x86-linux"
-IUSE="+dap doc examples hdf +hdf5 mpi szip test tools"
-RESTRICT="!test? ( test )"
-
-RDEPEND="dev-libs/libxml2
- dap? ( net-misc/curl:0= )
- hdf? (
- sci-libs/hdf:0=
- sci-libs/hdf5:0=
- virtual/jpeg
- )
- hdf5? ( sci-libs/hdf5:0=[hl(+),mpi=,szip=,zlib] )"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig
- doc? ( app-doc/doxygen[dot] )"
-
-REQUIRED_USE="
- test? ( tools )
- szip? ( hdf5 )
- mpi? ( hdf5 )"
-
-PATCHES=(
- "${FILESDIR}/${PN}-4.8.1-big-endian-build.patch"
- "${FILESDIR}/${PN}-4.7.4-big-endian-test.patch"
-)
-
-src_prepare() {
- # skip test that requires network
- sed -i -e '/run_get_hdf4_files/d' hdf4_test/CMakeLists.txt || die
-
- cmake_src_prepare
-}
-
-src_configure() {
- use mpi && export CC=mpicc
-
- # Temporary workaround for test breakage
- # https://github.com/Unidata/netcdf-c/issues/1983
- # bug #827042
- append-flags -fno-strict-aliasing
-
- local mycmakeargs=(
- -DENABLE_DAP_REMOTE_TESTS=OFF
- # Enable for >4.8.1 (not yet in a release)
- #-DENABLE_LIBXML2=ON
- -DBUILD_UTILITIES=$(usex tools)
- -DENABLE_DAP=$(usex dap)
- -DENABLE_DOXYGEN=$(usex doc)
- -DENABLE_EXAMPLES=$(usex examples)
- -DENABLE_HDF4=$(usex hdf)
- -DENABLE_NETCDF_4=$(usex hdf5)
- -DENABLE_TESTS=$(usex test)
- )
-
- cmake_src_configure
-}
-
-src_test() {
- # fails parallel tests: bug #621486
- cmake_src_test -j1
-}
diff --git a/sci-libs/netcdf/netcdf-4.8.1-r2.ebuild b/sci-libs/netcdf/netcdf-4.8.1-r2.ebuild
deleted file mode 100644
index d4e17743df68..000000000000
--- a/sci-libs/netcdf/netcdf-4.8.1-r2.ebuild
+++ /dev/null
@@ -1,83 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit cmake flag-o-matic
-
-DESCRIPTION="Scientific library and interface for array oriented data access"
-HOMEPAGE="https://www.unidata.ucar.edu/software/netcdf/"
-SRC_URI="https://github.com/Unidata/netcdf-c/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-S="${WORKDIR}/${PN}-c-${PV}"
-
-LICENSE="UCAR-Unidata"
-# SONAME of libnetcdf.so
-SLOT="0/19"
-KEYWORDS="amd64 ~arm ~arm64 ~ia64 ~ppc ppc64 -riscv ~x86 ~amd64-linux ~x86-linux"
-IUSE="+dap doc examples hdf +hdf5 mpi szip test tools"
-RESTRICT="!test? ( test )"
-
-RDEPEND="dev-libs/libxml2
- dap? ( net-misc/curl:0= )
- hdf? (
- media-libs/libjpeg-turbo:=
- sci-libs/hdf:0=
- sci-libs/hdf5:0=
- )
- hdf5? ( sci-libs/hdf5:0=[hl(+),mpi=,szip=,zlib] )"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig
- doc? ( app-doc/doxygen[dot] )"
-
-REQUIRED_USE="
- test? ( tools )
- szip? ( hdf5 )
- mpi? ( hdf5 )"
-
-PATCHES=(
- "${FILESDIR}/${PN}-4.8.1-big-endian-build.patch"
- "${FILESDIR}/${PN}-4.7.4-big-endian-test.patch"
-)
-
-src_prepare() {
- # skip test that requires network
- sed -i -e '/run_get_hdf4_files/d' hdf4_test/CMakeLists.txt || die
-
- cmake_src_prepare
-}
-
-src_configure() {
- use mpi && export CC=mpicc
-
- # Temporary workaround for test breakage
- # https://github.com/Unidata/netcdf-c/issues/1983
- # bug #827042
- append-flags -fno-strict-aliasing
-
- local mycmakeargs=(
- -DENABLE_DAP_REMOTE_TESTS=OFF
- # Enable for >4.8.1 (not yet in a release)
- #-DENABLE_LIBXML2=ON
- -DBUILD_UTILITIES=$(usex tools)
- -DENABLE_DAP=$(usex dap)
- -DENABLE_DOXYGEN=$(usex doc)
- -DENABLE_EXAMPLES=$(usex examples)
- -DENABLE_HDF4=$(usex hdf)
- -DENABLE_NETCDF_4=$(usex hdf5)
- -DENABLE_TESTS=$(usex test)
- )
-
- cmake_src_configure
-}
-
-src_test() {
- # fails parallel tests: bug #621486
- cmake_src_test -j1
-}
-
-src_install() {
- cmake_src_install
-
- # bug #827188
- sed -i -e "s:${EPREFIX}/usr/$(get_libdir)/libdl.so;:dl;:" "${ED}/usr/$(get_libdir)/cmake/netCDF/netCDFTargets.cmake" || die
-}
^ permalink raw reply related [flat|nested] 3+ messages in thread
end of thread, other threads:[~2023-07-27 19:42 UTC | newest]
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