* [PR PATCH] hdf5: update to 1.14.4.3, fix cross.
@ 2024-08-17 22:58 tornaria
2024-08-18 2:45 ` [PR PATCH] [Updated] " tornaria
` (17 more replies)
0 siblings, 18 replies; 19+ messages in thread
From: tornaria @ 2024-08-17 22:58 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1653 bytes --]
There is a new pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
hdf5: update to 1.14.4.3, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **med: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 15126 bytes --]
From aa879330b369cdc619b1a6dfd66006d8c17f2c59 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/13] hdf5: update to 1.14.4.3, fix cross.
---
common/shlibs | 12 ++++++------
srcpkgs/hdf5/template | 22 +++++++++++++---------
2 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/common/shlibs b/common/shlibs
index 4b2660a025f11f..850ba926bff4b5 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2646,12 +2646,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.4.3_1
+libhdf5.so.310 hdf5-1.14.4.3_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5hl_fortran.so.310 hdf5-1.14.4.3_1
+libhdf5_fortran.so.310 hdf5-1.14.4.3_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index 915d287cd32f71..ce7521482ab418 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,26 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.5
-revision=2
+version=1.14.4.3
+revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-${version}.tar.gz"
-checksum=6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8
-nocross="https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=690c1db7ba0fed4ffac61709236675ffd99d95d191e8920ee79c58d7e7ea3361
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From b2faade060bf8dd3ca59a4c465e0063dcd73fab3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/13] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From c567453f112639511fe74b95aba4723ef8add767 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/13] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..4dc175dccf3eba 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/mariusmuja/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From 94f973fdb925f9e0526edf52832312e478047fd7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 04/13] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From d532aff9ca1e3e4b7f9d18bea25ae8c0706be4a1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 05/13] med: rebuild for hdf5
---
srcpkgs/med/template | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/srcpkgs/med/template b/srcpkgs/med/template
index 48f8d35c88bd7a..22363c36468a36 100644
--- a/srcpkgs/med/template
+++ b/srcpkgs/med/template
@@ -1,7 +1,7 @@
# Template file for 'med'
pkgname=med
version=4.1.0
-revision=4
+revision=5
build_style=gnu-configure
configure_args="--with-swig=yes --includedir=/usr/include/med"
hostmakedepends="gcc-fortran swig python3-setuptools"
@@ -14,8 +14,6 @@ homepage="https://www.salome-platform.org"
distfiles="http://files.salome-platform.org/Salome/other/med-${version}.tar.gz"
checksum=847db5d6fbc9ce6924cb4aea86362812c9a5ef6b9684377e4dd6879627651fce
-nocross="hdf5 is nocross"
-
post_extract() {
# The py-compile helper uses the imp module, removed in Python 3.12;
# besides, we don't want the module pre-compiled anyway, so just drop it
From 33918fafb341e8056089cd9a257f3b5493f580a4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 06/13] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From 7fb7249b541a1e4083a1d2de21feae701fcbed3e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 07/13] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 15 ++++++---------
1 file changed, 6 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 89106c53024a3d..22ff8422cfb979 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=2
+revision=3
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,10 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From 5eda3f5954a022faa431b5fb2b0e03e1cc441730 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 08/13] octave: rebuild for hdf5
---
srcpkgs/octave/template | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index b8f92fd8a6336d..6c316b7dd67ce7 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,7 +1,7 @@
# Template file for 'octave'
pkgname=octave
version=9.2.0
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config"
@@ -71,16 +71,12 @@ build_options_default="
fftw3
graphicsmagick
gui
+ hdf5
opengl
openmp
qhull
zlib"
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- build_options_default+=" hdf5"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
From 94ec5de930c0f6f227f4624c559e4f302b81d839 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 09/13] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index c77df7c1123719..d99772f94e7657 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,7 +1,7 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.11.0
-revision=2
+revision=3
build_style=python3-module
build_helper="numpy"
hostmakedepends="python3-setuptools python3-Cython0.29 python3-pkgconfig"
From 40b997e8094318ca26045b6527e8cb1cd02d3347 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 10/13] python3-tables: rebuild for hdf5
---
srcpkgs/python3-tables/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/python3-tables/template b/srcpkgs/python3-tables/template
index 38c93292ea4bf8..b7735fd298cf45 100644
--- a/srcpkgs/python3-tables/template
+++ b/srcpkgs/python3-tables/template
@@ -1,7 +1,7 @@
# Template file for 'python3-tables'
pkgname=python3-tables
version=3.7.0
-revision=4
+revision=5
build_style=python3-module
build_helper=numpy
# XXX: c-blosc (using internal for now)
From fecbfd7f0b72534bf9779226be7880e4e02bb319 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/13] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index 3e7f8009de1901..e6899e696c1ad9 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.36.3
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
From be79db8f2ba5303069cbc5a1c1461f0c29c1c0d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 12/13] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From 8c78f9a3283376f1e21fba17e3684f1780465816 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 13/13] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 189591d55725a7..5a3cae4dfb227e 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.2.6
-revision=3
+revision=4
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
@ 2024-08-18 2:45 ` tornaria
2024-08-18 16:19 ` tornaria
` (16 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2024-08-18 2:45 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1658 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
hdf5: update to 1.14.4.3, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **med: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 14013 bytes --]
From aa879330b369cdc619b1a6dfd66006d8c17f2c59 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.4.3, fix cross.
---
common/shlibs | 12 ++++++------
srcpkgs/hdf5/template | 22 +++++++++++++---------
2 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/common/shlibs b/common/shlibs
index 4b2660a025f11f..850ba926bff4b5 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2646,12 +2646,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.4.3_1
+libhdf5.so.310 hdf5-1.14.4.3_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5hl_fortran.so.310 hdf5-1.14.4.3_1
+libhdf5_fortran.so.310 hdf5-1.14.4.3_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index 915d287cd32f71..ce7521482ab418 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,26 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.5
-revision=2
+version=1.14.4.3
+revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-${version}.tar.gz"
-checksum=6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8
-nocross="https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=690c1db7ba0fed4ffac61709236675ffd99d95d191e8920ee79c58d7e7ea3361
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From b2faade060bf8dd3ca59a4c465e0063dcd73fab3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From c567453f112639511fe74b95aba4723ef8add767 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..4dc175dccf3eba 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/mariusmuja/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From 94f973fdb925f9e0526edf52832312e478047fd7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 04/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From 0931f230375b6b0b8cdcecd008d344eb4900aade Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 05/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From fdea000019cec38e6c65dfe941ea90d968a9a674 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 06/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 15 ++++++---------
1 file changed, 6 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 89106c53024a3d..22ff8422cfb979 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=2
+revision=3
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,10 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From c096b82ab273db2b40061c8120b4912364cf3737 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 07/12] octave: rebuild for hdf5
---
srcpkgs/octave/template | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index b8f92fd8a6336d..6c316b7dd67ce7 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,7 +1,7 @@
# Template file for 'octave'
pkgname=octave
version=9.2.0
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config"
@@ -71,16 +71,12 @@ build_options_default="
fftw3
graphicsmagick
gui
+ hdf5
opengl
openmp
qhull
zlib"
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- build_options_default+=" hdf5"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
From a73805d00f901c8312b5ae0b82e6857af4e528f8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index c77df7c1123719..d99772f94e7657 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,7 +1,7 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.11.0
-revision=2
+revision=3
build_style=python3-module
build_helper="numpy"
hostmakedepends="python3-setuptools python3-Cython0.29 python3-pkgconfig"
From af4a20c956659d03fc7e6f810edb22d371d4ebc0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 09/12] python3-tables: rebuild for hdf5
---
srcpkgs/python3-tables/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/python3-tables/template b/srcpkgs/python3-tables/template
index 38c93292ea4bf8..b7735fd298cf45 100644
--- a/srcpkgs/python3-tables/template
+++ b/srcpkgs/python3-tables/template
@@ -1,7 +1,7 @@
# Template file for 'python3-tables'
pkgname=python3-tables
version=3.7.0
-revision=4
+revision=5
build_style=python3-module
build_helper=numpy
# XXX: c-blosc (using internal for now)
From 567882125a9a22ca69f750a3405f1aa936b16c22 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index 3e7f8009de1901..e6899e696c1ad9 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.36.3
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
From 0c1b9af629917557abce5e3500c8dcd434409822 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From 525ea485259f83a5f3b635d41d1b43fe6e7c6109 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 12/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 189591d55725a7..5a3cae4dfb227e 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.2.6
-revision=3
+revision=4
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
2024-08-18 2:45 ` [PR PATCH] [Updated] " tornaria
@ 2024-08-18 16:19 ` tornaria
2024-08-18 20:39 ` [PR PATCH] [Updated] [WIP] " tornaria
` (15 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2024-08-18 16:19 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1658 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
hdf5: update to 1.14.4.3, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **med: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 16589 bytes --]
From 757fa6978d96160b54fe107a014a5212dcc05290 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.4.3, fix cross.
---
common/shlibs | 12 ++++++------
srcpkgs/hdf5/template | 22 +++++++++++++---------
2 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/common/shlibs b/common/shlibs
index 4b2660a025f11f..850ba926bff4b5 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2646,12 +2646,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.4.3_1
+libhdf5.so.310 hdf5-1.14.4.3_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5hl_fortran.so.310 hdf5-1.14.4.3_1
+libhdf5_fortran.so.310 hdf5-1.14.4.3_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index 915d287cd32f71..ce7521482ab418 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,26 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.5
-revision=2
+version=1.14.4.3
+revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-${version}.tar.gz"
-checksum=6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8
-nocross="https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=690c1db7ba0fed4ffac61709236675ffd99d95d191e8920ee79c58d7e7ea3361
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From 5eea3bb51892b1f68a08246471750f4c3143ce9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From dee8e40b6d5ea551ba6b2cb894f8759641a48d3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..4dc175dccf3eba 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/mariusmuja/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From 6f84f22ef947bc547139ad888319c7bbfefae5c1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 04/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From d82476a8a9f455ea248100325ceee2c7bebcb83d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 05/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From cc13da465e1d096bdf39d82dfe1d7b4971485738 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 06/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 18 ++++++++----------
1 file changed, 8 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 89106c53024a3d..8dc466d550fa03 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,19 +1,20 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=2
+revision=3
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
-DPython_NumPy_INCLUDE_DIR=/${py3_sitelib}/numpy/core/include/numpy"
-hostmakedepends="pkg-config bison swig python3-numpy python3-setuptools"
+hostmakedepends="pkg-config bison swig python3-numpy python3-setuptools
+ python3-devel"
makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
jasper-devel giflib-devel json-c-devel libcurl-devel libopenexr-devel
libjpeg-turbo-devel libpng-devel tiff-devel libqhull-devel libwebp-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +25,10 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From 8a0998e719eb658f6d257398ee10b6f8b8d388c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 07/12] octave: rebuild for hdf5
---
srcpkgs/octave/template | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index b8f92fd8a6336d..6c316b7dd67ce7 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,7 +1,7 @@
# Template file for 'octave'
pkgname=octave
version=9.2.0
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config"
@@ -71,16 +71,12 @@ build_options_default="
fftw3
graphicsmagick
gui
+ hdf5
opengl
openmp
qhull
zlib"
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- build_options_default+=" hdf5"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
From fd6f486f1daddd5556d7841d54041a3d0e099cb7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index c77df7c1123719..cfd3a8b3fc3c06 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,10 +1,11 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.11.0
-revision=2
+revision=3
build_style=python3-module
build_helper="numpy"
-hostmakedepends="python3-setuptools python3-Cython0.29 python3-pkgconfig"
+hostmakedepends="python3-setuptools python3-Cython0.29 python3-pkgconfig
+ hdf5-devel"
makedepends="python3-devel hdf5-devel"
depends="python3-numpy"
short_desc="HDF5 for Python"
From 0224429a0d598732f6cda2ba866bc9a7dd72e0e2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 09/12] python3-tables: rebuild for hdf5
---
srcpkgs/python3-tables/patches/numpy-2.0.patch | 2 +-
srcpkgs/python3-tables/template | 9 ++++++++-
2 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-tables/patches/numpy-2.0.patch b/srcpkgs/python3-tables/patches/numpy-2.0.patch
index 58ad624c994975..36d2a6151a3c57 100644
--- a/srcpkgs/python3-tables/patches/numpy-2.0.patch
+++ b/srcpkgs/python3-tables/patches/numpy-2.0.patch
@@ -98,7 +98,7 @@ diff -ur a/tables/index.py b/tables/index.py
# First normalize the number of rows
offset2 = (nrow % self.nslicesblock) * slicesize // lbucket
- idx += offset2
-+ assert offset2 < 2**(indsize*8)
++ assert offset2 < 2**(indsize*8)
+ idx += np.asarray(offset2).astype(idx.dtype)
# Add the last row at the beginning of arr & idx (if needed)
if (indsize == 8 and nelementsILR > 0):
diff --git a/srcpkgs/python3-tables/template b/srcpkgs/python3-tables/template
index 38c93292ea4bf8..3d47b93cd2805a 100644
--- a/srcpkgs/python3-tables/template
+++ b/srcpkgs/python3-tables/template
@@ -1,7 +1,7 @@
# Template file for 'python3-tables'
pkgname=python3-tables
version=3.7.0
-revision=4
+revision=5
build_style=python3-module
build_helper=numpy
# XXX: c-blosc (using internal for now)
@@ -16,6 +16,13 @@ homepage="http://www.pytables.org/"
changelog="http://www.pytables.org/release_notes.html"
distfiles="${PYPI_SITE}/t/tables/tables-${version}.tar.gz"
checksum=e92a887ad6f2a983e564a69902de4a7645c30069fc01abd353ec5da255c5e1fe
+make_check=no # broken
+
+if [ -n "$CROSS_BUILD" ]; then
+ # cross build will detect cpu from host, override
+ export DISABLE_SSE2=1
+ export DISABLE_AVX2=1
+fi
post_extract() {
# Make sure Cython is run during build
From 58c5d200df37b532d504cbb562ff6d1fa1ae2568 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index 3e7f8009de1901..ef3e5911b78d11 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.36.3
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
@@ -30,6 +30,7 @@ license="GPL-2.0-only"
homepage="https://qgis.org"
distfiles="https://github.com/qgis/QGIS/archive/final-${version//./_}.tar.gz"
checksum=8fd8add9ac36ff3e9eb5e4cae35a8f9eb40c57a7fe9ccebbba22708afe2d4555
+nocross="due to grass"
post_install() {
mv ${DESTDIR}/usr/share/qgis/python ${DESTDIR}/usr/lib/qgis/
From 827df838c8d91fcccae2136eb60c3e71a60d9149 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From 6e115274093c8c19c9356e7db6cb43c076a3a949 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 12/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 189591d55725a7..e15764df02f173 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.2.6
-revision=3
+revision=4
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
@@ -27,6 +27,7 @@ license="BSD-3-Clause"
homepage="https://www.vtk.org"
distfiles="https://www.vtk.org/files/release/${version:0:3}/VTK-${version}.tar.gz"
checksum=06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12
+nocross="It seems to need vtk compile tools for the host"
if [ "$XBPS_TARGET_LIBC" = "musl" ]; then
makedepends+=" libexecinfo-devel"
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] [WIP] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
2024-08-18 2:45 ` [PR PATCH] [Updated] " tornaria
2024-08-18 16:19 ` tornaria
@ 2024-08-18 20:39 ` tornaria
2024-08-18 22:12 ` tornaria
` (14 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2024-08-18 20:39 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1742 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
[WIP] hdf5: update to 1.14.4.3, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 17108 bytes --]
From 757fa6978d96160b54fe107a014a5212dcc05290 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.4.3, fix cross.
---
common/shlibs | 12 ++++++------
srcpkgs/hdf5/template | 22 +++++++++++++---------
2 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/common/shlibs b/common/shlibs
index 4b2660a025f11f..850ba926bff4b5 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2646,12 +2646,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.4.3_1
+libhdf5.so.310 hdf5-1.14.4.3_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5hl_fortran.so.310 hdf5-1.14.4.3_1
+libhdf5_fortran.so.310 hdf5-1.14.4.3_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index 915d287cd32f71..ce7521482ab418 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,26 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.5
-revision=2
+version=1.14.4.3
+revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-${version}.tar.gz"
-checksum=6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8
-nocross="https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=690c1db7ba0fed4ffac61709236675ffd99d95d191e8920ee79c58d7e7ea3361
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From 5eea3bb51892b1f68a08246471750f4c3143ce9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From dee8e40b6d5ea551ba6b2cb894f8759641a48d3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..4dc175dccf3eba 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/mariusmuja/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From 6f84f22ef947bc547139ad888319c7bbfefae5c1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 04/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From d82476a8a9f455ea248100325ceee2c7bebcb83d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 05/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From 058a33746fc36f8713051fa1f5b52deb97a64882 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 06/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 89106c53024a3d..8d7995a0af4c6a 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=2
+revision=3
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,12 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+CXXFLAGS=-I$XBPS_CROSS_BASE/usr/include/python$py3_ver
+
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From 9e9f5d0507c427a7053958ab24eb2f9f520bd9b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 07/12] octave: rebuild for hdf5
---
srcpkgs/octave/template | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index b8f92fd8a6336d..6c316b7dd67ce7 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,7 +1,7 @@
# Template file for 'octave'
pkgname=octave
version=9.2.0
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config"
@@ -71,16 +71,12 @@ build_options_default="
fftw3
graphicsmagick
gui
+ hdf5
opengl
openmp
qhull
zlib"
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- build_options_default+=" hdf5"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
From d24b3042844a57248fc4db8cd8f4f679b5167464 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index c77df7c1123719..cfd3a8b3fc3c06 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,10 +1,11 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.11.0
-revision=2
+revision=3
build_style=python3-module
build_helper="numpy"
-hostmakedepends="python3-setuptools python3-Cython0.29 python3-pkgconfig"
+hostmakedepends="python3-setuptools python3-Cython0.29 python3-pkgconfig
+ hdf5-devel"
makedepends="python3-devel hdf5-devel"
depends="python3-numpy"
short_desc="HDF5 for Python"
From 610a33b833a4e7f891b95c56bfe14973d0d51642 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 09/12] python3-tables: rebuild for hdf5
---
srcpkgs/python3-tables/patches/numpy-2.0.patch | 2 +-
srcpkgs/python3-tables/template | 9 ++++++++-
2 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-tables/patches/numpy-2.0.patch b/srcpkgs/python3-tables/patches/numpy-2.0.patch
index 58ad624c994975..36d2a6151a3c57 100644
--- a/srcpkgs/python3-tables/patches/numpy-2.0.patch
+++ b/srcpkgs/python3-tables/patches/numpy-2.0.patch
@@ -98,7 +98,7 @@ diff -ur a/tables/index.py b/tables/index.py
# First normalize the number of rows
offset2 = (nrow % self.nslicesblock) * slicesize // lbucket
- idx += offset2
-+ assert offset2 < 2**(indsize*8)
++ assert offset2 < 2**(indsize*8)
+ idx += np.asarray(offset2).astype(idx.dtype)
# Add the last row at the beginning of arr & idx (if needed)
if (indsize == 8 and nelementsILR > 0):
diff --git a/srcpkgs/python3-tables/template b/srcpkgs/python3-tables/template
index 38c93292ea4bf8..3d47b93cd2805a 100644
--- a/srcpkgs/python3-tables/template
+++ b/srcpkgs/python3-tables/template
@@ -1,7 +1,7 @@
# Template file for 'python3-tables'
pkgname=python3-tables
version=3.7.0
-revision=4
+revision=5
build_style=python3-module
build_helper=numpy
# XXX: c-blosc (using internal for now)
@@ -16,6 +16,13 @@ homepage="http://www.pytables.org/"
changelog="http://www.pytables.org/release_notes.html"
distfiles="${PYPI_SITE}/t/tables/tables-${version}.tar.gz"
checksum=e92a887ad6f2a983e564a69902de4a7645c30069fc01abd353ec5da255c5e1fe
+make_check=no # broken
+
+if [ -n "$CROSS_BUILD" ]; then
+ # cross build will detect cpu from host, override
+ export DISABLE_SSE2=1
+ export DISABLE_AVX2=1
+fi
post_extract() {
# Make sure Cython is run during build
From f244fc6458c5e2cce2a92c7efa280a6619bcb161 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index 3e7f8009de1901..ef3e5911b78d11 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.36.3
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
@@ -30,6 +30,7 @@ license="GPL-2.0-only"
homepage="https://qgis.org"
distfiles="https://github.com/qgis/QGIS/archive/final-${version//./_}.tar.gz"
checksum=8fd8add9ac36ff3e9eb5e4cae35a8f9eb40c57a7fe9ccebbba22708afe2d4555
+nocross="due to grass"
post_install() {
mv ${DESTDIR}/usr/share/qgis/python ${DESTDIR}/usr/lib/qgis/
From 95ce21c706729131fd763f4fccf7900e3a5272de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From adce41c1731c0f5b214f2ab46306b08d456dd085 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 12/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 189591d55725a7..b9c7b95c99af34 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.2.6
-revision=3
+revision=4
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
@@ -18,7 +18,7 @@ configure_args="-DBUILD_SHARED_LIBS=ON -DVTK_FORBID_DOWNLOADS=ON
# vtk forks libharu, bumps to v2.4.0, and requires libharu>=2.4.0
makedepends="zlib-devel freetype-devel liblz4-devel expat-devel MesaLib-devel
libXt-devel libjpeg-turbo-devel tiff-devel hdf5-devel netcdf-devel
- libxml2-devel jsoncpp-devel openmpi-devel libogg-devel libtheora-devel
+ libxml2-devel jsoncpp-devel libogg-devel libtheora-devel
eigen double-conversion-devel glew-devel pugixml-devel sqlite-devel
gl2ps-devel proj-devel python3-devel json-c++ fmt-devel"
short_desc="System for 3D computer graphics, image processing, and visualization"
@@ -27,6 +27,15 @@ license="BSD-3-Clause"
homepage="https://www.vtk.org"
distfiles="https://www.vtk.org/files/release/${version:0:3}/VTK-${version}.tar.gz"
checksum=06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12
+nocross="It seems to need vtk compile tools for the host"
+
+case "$XBPS_TARGET_MACHINE" in
+ # List of supported architectures copied from openmpi.
+ x86_64*|aarch64*|ppc64*|riscv64*)
+ makedepends+=" openmpi-devel"
+ ;;
+esac
+
if [ "$XBPS_TARGET_LIBC" = "musl" ]; then
makedepends+=" libexecinfo-devel"
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] [WIP] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (2 preceding siblings ...)
2024-08-18 20:39 ` [PR PATCH] [Updated] [WIP] " tornaria
@ 2024-08-18 22:12 ` tornaria
2024-10-01 0:43 ` Calandracas606
` (13 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2024-08-18 22:12 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1742 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
[WIP] hdf5: update to 1.14.4.3, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
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From 757fa6978d96160b54fe107a014a5212dcc05290 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.4.3, fix cross.
---
common/shlibs | 12 ++++++------
srcpkgs/hdf5/template | 22 +++++++++++++---------
2 files changed, 19 insertions(+), 15 deletions(-)
diff --git a/common/shlibs b/common/shlibs
index 4b2660a025f11f..850ba926bff4b5 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2646,12 +2646,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.4.3_1
+libhdf5.so.310 hdf5-1.14.4.3_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5_cpp.so.310 hdf5-1.14.4.3_1
+libhdf5hl_fortran.so.310 hdf5-1.14.4.3_1
+libhdf5_fortran.so.310 hdf5-1.14.4.3_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index 915d287cd32f71..ce7521482ab418 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,26 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.5
-revision=2
+version=1.14.4.3
+revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-${version}.tar.gz"
-checksum=6d4ce8bf902a97b050f6f491f4268634e252a63dadd6656a1a9be5b7b7726fa8
-nocross="https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=690c1db7ba0fed4ffac61709236675ffd99d95d191e8920ee79c58d7e7ea3361
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From 5eea3bb51892b1f68a08246471750f4c3143ce9c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From dee8e40b6d5ea551ba6b2cb894f8759641a48d3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..4dc175dccf3eba 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/mariusmuja/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From 6f84f22ef947bc547139ad888319c7bbfefae5c1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 04/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From d82476a8a9f455ea248100325ceee2c7bebcb83d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 05/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From 058a33746fc36f8713051fa1f5b52deb97a64882 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 06/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 89106c53024a3d..8d7995a0af4c6a 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=2
+revision=3
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,12 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+CXXFLAGS=-I$XBPS_CROSS_BASE/usr/include/python$py3_ver
+
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From 9e9f5d0507c427a7053958ab24eb2f9f520bd9b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 07/12] octave: rebuild for hdf5
---
srcpkgs/octave/template | 8 ++------
1 file changed, 2 insertions(+), 6 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index b8f92fd8a6336d..6c316b7dd67ce7 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,7 +1,7 @@
# Template file for 'octave'
pkgname=octave
version=9.2.0
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config"
@@ -71,16 +71,12 @@ build_options_default="
fftw3
graphicsmagick
gui
+ hdf5
opengl
openmp
qhull
zlib"
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- build_options_default+=" hdf5"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
From d9a802395e412ad4e6dd2c3583bb8aba944f7896 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 11 +++++++++--
1 file changed, 9 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index c77df7c1123719..1f80778121ee4f 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,10 +1,11 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.11.0
-revision=2
+revision=3
build_style=python3-module
build_helper="numpy"
-hostmakedepends="python3-setuptools python3-Cython0.29 python3-pkgconfig"
+hostmakedepends="python3-setuptools python3-Cython0.29 python3-pkgconfig
+ hdf5-devel"
makedepends="python3-devel hdf5-devel"
depends="python3-numpy"
short_desc="HDF5 for Python"
@@ -16,6 +17,12 @@ checksum=7b7e8f78072a2edec87c9836f25f34203fd492a4475709a18b417a33cfb21fa9
# Tests require unpackaged pytest-mpi
make_check=no
+if [ -n "$CROSS_BUILD" ] && [ "$XBPS_TARGET_WORDSIZE" = "32" ]; then
+ # numpy.complex256 is N/A on 32 bit; it is misdetected if host is 64 bit
+ # we need `DEF COMPLEX256_SUPPORT = False`, this seems the easiest way
+ export CIBW_ARCHS_MACOS=arm64
+fi
+
pre_build() {
# Build in parallel
make_build_args+=" ${makejobs}"
From b581452cd4984930509adac30384eb310038d7ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 09/12] python3-tables: rebuild for hdf5
---
srcpkgs/python3-tables/patches/numpy-2.0.patch | 2 +-
srcpkgs/python3-tables/template | 9 ++++++++-
2 files changed, 9 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-tables/patches/numpy-2.0.patch b/srcpkgs/python3-tables/patches/numpy-2.0.patch
index 58ad624c994975..36d2a6151a3c57 100644
--- a/srcpkgs/python3-tables/patches/numpy-2.0.patch
+++ b/srcpkgs/python3-tables/patches/numpy-2.0.patch
@@ -98,7 +98,7 @@ diff -ur a/tables/index.py b/tables/index.py
# First normalize the number of rows
offset2 = (nrow % self.nslicesblock) * slicesize // lbucket
- idx += offset2
-+ assert offset2 < 2**(indsize*8)
++ assert offset2 < 2**(indsize*8)
+ idx += np.asarray(offset2).astype(idx.dtype)
# Add the last row at the beginning of arr & idx (if needed)
if (indsize == 8 and nelementsILR > 0):
diff --git a/srcpkgs/python3-tables/template b/srcpkgs/python3-tables/template
index 38c93292ea4bf8..3d47b93cd2805a 100644
--- a/srcpkgs/python3-tables/template
+++ b/srcpkgs/python3-tables/template
@@ -1,7 +1,7 @@
# Template file for 'python3-tables'
pkgname=python3-tables
version=3.7.0
-revision=4
+revision=5
build_style=python3-module
build_helper=numpy
# XXX: c-blosc (using internal for now)
@@ -16,6 +16,13 @@ homepage="http://www.pytables.org/"
changelog="http://www.pytables.org/release_notes.html"
distfiles="${PYPI_SITE}/t/tables/tables-${version}.tar.gz"
checksum=e92a887ad6f2a983e564a69902de4a7645c30069fc01abd353ec5da255c5e1fe
+make_check=no # broken
+
+if [ -n "$CROSS_BUILD" ]; then
+ # cross build will detect cpu from host, override
+ export DISABLE_SSE2=1
+ export DISABLE_AVX2=1
+fi
post_extract() {
# Make sure Cython is run during build
From b279ab61e9028c867356ae0f2c6b50b0fe865c4f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index 3e7f8009de1901..ef3e5911b78d11 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.36.3
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
@@ -30,6 +30,7 @@ license="GPL-2.0-only"
homepage="https://qgis.org"
distfiles="https://github.com/qgis/QGIS/archive/final-${version//./_}.tar.gz"
checksum=8fd8add9ac36ff3e9eb5e4cae35a8f9eb40c57a7fe9ccebbba22708afe2d4555
+nocross="due to grass"
post_install() {
mv ${DESTDIR}/usr/share/qgis/python ${DESTDIR}/usr/lib/qgis/
From 1aa5c8a332bc2e366471fd997a615f9413b500c6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From d8fb1aca68ee38f9c835edff7d6e2456df8a1a4f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 12/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 13 +++++++++++--
1 file changed, 11 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 189591d55725a7..b9c7b95c99af34 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.2.6
-revision=3
+revision=4
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
@@ -18,7 +18,7 @@ configure_args="-DBUILD_SHARED_LIBS=ON -DVTK_FORBID_DOWNLOADS=ON
# vtk forks libharu, bumps to v2.4.0, and requires libharu>=2.4.0
makedepends="zlib-devel freetype-devel liblz4-devel expat-devel MesaLib-devel
libXt-devel libjpeg-turbo-devel tiff-devel hdf5-devel netcdf-devel
- libxml2-devel jsoncpp-devel openmpi-devel libogg-devel libtheora-devel
+ libxml2-devel jsoncpp-devel libogg-devel libtheora-devel
eigen double-conversion-devel glew-devel pugixml-devel sqlite-devel
gl2ps-devel proj-devel python3-devel json-c++ fmt-devel"
short_desc="System for 3D computer graphics, image processing, and visualization"
@@ -27,6 +27,15 @@ license="BSD-3-Clause"
homepage="https://www.vtk.org"
distfiles="https://www.vtk.org/files/release/${version:0:3}/VTK-${version}.tar.gz"
checksum=06fc8d49c4e56f498c40fcb38a563ed8d4ec31358d0101e8988f0bb4d539dd12
+nocross="It seems to need vtk compile tools for the host"
+
+case "$XBPS_TARGET_MACHINE" in
+ # List of supported architectures copied from openmpi.
+ x86_64*|aarch64*|ppc64*|riscv64*)
+ makedepends+=" openmpi-devel"
+ ;;
+esac
+
if [ "$XBPS_TARGET_LIBC" = "musl" ]; then
makedepends+=" libexecinfo-devel"
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [WIP] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (3 preceding siblings ...)
2024-08-18 22:12 ` tornaria
@ 2024-10-01 0:43 ` Calandracas606
2024-12-30 2:01 ` github-actions
` (12 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: Calandracas606 @ 2024-10-01 0:43 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 2137 bytes --]
New comment by Calandracas606 on void-packages repository
https://github.com/void-linux/void-packages/pull/51891#issuecomment-2384561411
Comment:
for med, the distfiles link is broken, and its not available on a public git repository
I've gotten med to build using debian's repack, and their patches: https://salsa.debian.org/science-team/med-fichier
```diff
diff --git a/srcpkgs/med/template b/srcpkgs/med/template
index 48f8d35c88b..f8961c5cfa6 100644
--- a/srcpkgs/med/template
+++ b/srcpkgs/med/template
@@ -1,20 +1,21 @@
# Template file for 'med'
pkgname=med
-version=4.1.0
-revision=4
+version=4.1.0+repack5
+revision=5
build_style=gnu-configure
-configure_args="--with-swig=yes --includedir=/usr/include/med"
-hostmakedepends="gcc-fortran swig python3-setuptools"
+configure_args="--with-swig=yes --includedir=/usr/include/med --disable-dependency-tracking"
+hostmakedepends="gcc-fortran swig python3-setuptools automake"
makedepends="hdf5-devel python3-devel tk-devel"
depends="tk" # xmdump* are wish scripts
short_desc="Data Modelization and Exchanges"
maintainer="Piraty <mail@piraty.dev>"
license="GPL-3.0-only, LGPL-3.0-only"
homepage="https://www.salome-platform.org"
-distfiles="http://files.salome-platform.org/Salome/other/med-${version}.tar.gz"
-checksum=847db5d6fbc9ce6924cb4aea86362812c9a5ef6b9684377e4dd6879627651fce
+distfiles="https://salsa.debian.org/science-team/med-fichier/-/archive/debian/${version/repack/repack-}/med-fichier-debian-${version/repack/repack-}.tar.gz"
+checksum=7aa248cf8d6ad78d898ae74b9a6809a56599486efc3cdc21d3c9b43b651a19bd
-nocross="hdf5 is nocross"
+CFLAGS="-DH5_USE_110_API"
+CXXFLAGS="-DH5_USE_110_API"
post_extract() {
# The py-compile helper uses the imp module, removed in Python 3.12;
@@ -26,6 +27,17 @@ post_extract() {
EOF
}
+post_patch() {
+ cd $wrksrc
+ for _file in ${wrksrc}/debian/patches/*.patch; do
+ patch -Np1 < $_file
+ done
+}
+
+pre_configure() {
+ ./bootstrap
+}
+
libmed-devel_package() {
short_desc+=" library - development files"
depends="libmed>=${version}_${revision}"
```
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [WIP] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (4 preceding siblings ...)
2024-10-01 0:43 ` Calandracas606
@ 2024-12-30 2:01 ` github-actions
2025-01-13 2:02 ` [PR PATCH] [Closed]: " github-actions
` (11 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: github-actions @ 2024-12-30 2:01 UTC (permalink / raw)
To: ml
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New comment by github-actions[bot] on void-packages repository
https://github.com/void-linux/void-packages/pull/51891#issuecomment-2564949926
Comment:
Pull Requests become stale 90 days after last activity and are closed 14 days after that. If this pull request is still relevant bump it or assign it.
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Closed]: [WIP] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (5 preceding siblings ...)
2024-12-30 2:01 ` github-actions
@ 2025-01-13 2:02 ` github-actions
2025-02-11 13:46 ` classabbyamp
` (10 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: github-actions @ 2025-01-13 2:02 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1587 bytes --]
There's a closed pull request on the void-packages repository
[WIP] hdf5: update to 1.14.4.3, fix cross.
https://github.com/void-linux/void-packages/pull/51891
Description:
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Closed]: [WIP] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (6 preceding siblings ...)
2025-01-13 2:02 ` [PR PATCH] [Closed]: " github-actions
@ 2025-02-11 13:46 ` classabbyamp
2025-02-12 0:40 ` [PR PATCH] [Updated] " tornaria
` (9 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: classabbyamp @ 2025-02-11 13:46 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1587 bytes --]
There's a closed pull request on the void-packages repository
[WIP] hdf5: update to 1.14.4.3, fix cross.
https://github.com/void-linux/void-packages/pull/51891
Description:
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] [WIP] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (7 preceding siblings ...)
2025-02-11 13:46 ` classabbyamp
@ 2025-02-12 0:40 ` tornaria
2025-02-12 3:02 ` tornaria
` (8 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2025-02-12 0:40 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1742 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
[WIP] hdf5: update to 1.14.4.3, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 24467 bytes --]
From 1a7118603469f9c952ab90e1988c7b05a4b01015 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.6, fix cross.
---
common/shlibs | 12 ++++++------
srcpkgs/hdf5/template | 21 +++++++++++++--------
2 files changed, 19 insertions(+), 14 deletions(-)
diff --git a/common/shlibs b/common/shlibs
index cc24170f5ec2f7..ddaafb61f88d21 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2648,12 +2648,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.6_1
+libhdf5.so.310 hdf5-1.14.6_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.6_1
+libhdf5_cpp.so.310 hdf5-1.14.6_1
+libhdf5hl_fortran.so.310 hdf5-1.14.6_1
+libhdf5_fortran.so.310 hdf5-1.14.6_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index a2ea9fcd797639..b035e8a5cd8c0b 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,27 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.11
+version=1.14.6
revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://github.com/HDFGroup/hdf5/archive/hdf5-${version//./_}.tar.gz"
-checksum=4ef6375fc7d8c54dcd66e9bc35a7a3580d33cd8878bdf21ad1eb388a43863159
-nocross="https://web.archive.org/web/20230924050239/https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+changelog="https://github.com/HDFGroup/hdf5/releases"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=09ee1c671a87401a5201c06106650f62badeea5a3b3941e9b1e2e1e08317357f
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From 5e48d8749fa764b8a3275960144378882ab1e3cc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From a945271efb483885909143205cca734629505298 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..9e4f38f91e2bad 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/flann-lib/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From f57b19741f80ba3a6a9e4ac9d1d3230e5c2bd987 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 11 Feb 2025 21:29:29 -0300
Subject: [PATCH 04/12] med: rebuild for hdf5
---
srcpkgs/med/patches/hdf5-1.14.patch | 99 ++++++++++++++++++++++++++
srcpkgs/med/patches/hdf5-version.patch | 17 +++++
srcpkgs/med/template | 3 +-
3 files changed, 118 insertions(+), 1 deletion(-)
create mode 100644 srcpkgs/med/patches/hdf5-1.14.patch
create mode 100644 srcpkgs/med/patches/hdf5-version.patch
diff --git a/srcpkgs/med/patches/hdf5-1.14.patch b/srcpkgs/med/patches/hdf5-1.14.patch
new file mode 100644
index 00000000000000..4d72add6b9fce9
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-1.14.patch
@@ -0,0 +1,99 @@
+https://salsa.debian.org/science-team/med-fichier/-/blob/master/debian/patches/hdf5-1.14.patch
+
+Index: med-fichier/config/med_check_hdf5.m4
+===================================================================
+--- med-fichier.orig/config/med_check_hdf5.m4
++++ med-fichier/config/med_check_hdf5.m4
+@@ -134,12 +134,6 @@ AC_REQUIRE([AC_PROG_GREP])
+ H5_VER_MINOR=` grep '#define *H5_VERS_MINOR' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_MINOR[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ H5_VER_RELEASE=`grep '#define *H5_VERS_RELEASE' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_RELEASE[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ HDF5_VERSION=` expr 10000 \* ${H5_VER_MAJOR} + 100 \* ${H5_VER_MINOR} + ${H5_VER_RELEASE} `
+- test "0${HDF5_VERSION}" -gt "11100" || test "0${HDF5_VERSION}" -lt "11002" && AC_MSG_ERROR([
+-This HDF5 version ${H5_VER_MAJOR}.${H5_VER_MINOR}.${H5_VER_RELEASE} must not be used with med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE}.
+-The HDF5 library version used by med-fichier${MED_NUM_MAJEUR}.y.z MUST NOT be > 1.10 and have to be at least HDF${HDF_VERSION_REF}.
+-DO NOT TRY TO COMPILE med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE} version with an HDF5 library which would generate an hdf5 file not compliant with HDF5-${HDF_VERSION_MAJOR_REF}.${HDF_VERSION_MINOR_REF}.z library.
+-This would BREAK med-fichier compatibility between files with the same revision number !
+- ])
+ else
+ ## In case user explicitly ask to not use hdf5 !
+ AC_MSG_WARN([Can't compile MED without hdf5])
+Index: med-fichier/src/ci/MEDfileCompatibility.c
+===================================================================
+--- med-fichier.orig/src/ci/MEDfileCompatibility.c
++++ med-fichier/src/ci/MEDfileCompatibility.c
+@@ -15,7 +15,6 @@
+ * along with MED. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+-
+ #include <med.h>
+ #include <med_config.h>
+ #include <med_outils.h>
+@@ -71,7 +70,7 @@ MEDfileCompatibility(const char* const f
+ _hversionMMR=10000*_hmajeur+100*_hmineur+_hrelease;
+ /* ISCRUTE(_hversionMMR); */
+ /* ISCRUTE(HDF_VERSION_NUM_REF); */
+- if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur == HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
++ if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur >= HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
+
+ /* TODO : Vérifier si la version mineure HDF du fichier est supérieure
+ à la version mineure de la bibliothèque HDF utilisée :
+@@ -114,8 +113,8 @@ MEDfileCompatibility(const char* const f
+ #error "Don't forget to update the test version here when you change the major version of the library !"
+ #endif
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
+-#error "Cf. _MEDfileCreate ..."
++#warning "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
++#warning "Cf. _MEDfileCreate ..."
+ #endif
+
+ SORTIE:
+Index: med-fichier/src/hdfi/_MEDfileCreate.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileCreate.c
++++ med-fichier/src/hdfi/_MEDfileCreate.c
+@@ -132,7 +132,7 @@ med_idt _MEDfileCreate(const char * cons
+ {
+ case 0: _release = MED_40_LATEST_RELEASE; break;
+ #if (MED_NUM_MINEUR == 0) && (MED_NUM_RELEASE > 1)
+-#error "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
++#warning "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
+ #endif
+ /* case 1: _release = 0; break; */
+ /* case 2: _release = 1; break; */
+@@ -160,7 +160,7 @@ med_idt _MEDfileCreate(const char * cons
+ * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18 ) ) {
+Index: med-fichier/src/hdfi/_MEDfileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileOpen.c
++++ med-fichier/src/hdfi/_MEDfileOpen.c
+@@ -73,7 +73,7 @@ med_idt _MEDfileOpen(const char * const
+ • The creation order tracking property, H5P_CRT_ORDER_TRACKED, has been set in the group creation property list (see H5Pset_link_creation_order).
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ /* L'avantage de bloquer le modèle interne HDF5
+ est que l'on peut modifier des fichiers med de différentes versions majeures de fichiers.
+Index: med-fichier/src/hdfi/_MEDmemFileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDmemFileOpen.c
++++ med-fichier/src/hdfi/_MEDmemFileOpen.c
+@@ -435,7 +435,7 @@ med_idt _MEDmemFileOpen(const char * con
+ }
+
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18) ) {
+ MED_ERR_(_fid,MED_ERR_INIT,MED_ERR_PROPERTY,MED_ERR_FILEVERSION_MSG);
diff --git a/srcpkgs/med/patches/hdf5-version.patch b/srcpkgs/med/patches/hdf5-version.patch
new file mode 100644
index 00000000000000..36db2c6689906e
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-version.patch
@@ -0,0 +1,17 @@
+Don't complain on hdf5, it works with hdf5 1.14 using `-DH5_USE_110_API=1`
+
+--- a/config/cmake_files/medMacros.cmake
++++ b/config/cmake_files/medMacros.cmake
+@@ -447,9 +447,9 @@
+ ##
+ ## Requires 1.10.x version
+ ##
+- IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
+- MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
+- ENDIF()
++ # IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
++ # MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
++ # ENDIF()
+ ##
+ ##
+
diff --git a/srcpkgs/med/template b/srcpkgs/med/template
index cc553adb493e68..85151578d68825 100644
--- a/srcpkgs/med/template
+++ b/srcpkgs/med/template
@@ -14,7 +14,8 @@ homepage="https://www.salome-platform.org"
distfiles="https://github.com/chennes/med/archive/v${version}.tar.gz"
checksum=ee8b3b6d46bfee25c1d289308b16c7f248d1339161fd5448339382125e6119ad
-nocross="hdf5 is nocross"
+# uses hdf5 old api
+CFLAGS+=" -DH5_USE_110_API=1"
post_extract() {
# The py-compile helper uses the imp module, removed in Python 3.12;
From 3aaa3a59f52a0ead5700dece16ba48503dab7aab Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 05/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From a5767bc025ebd776f3d4e1858d99d0e4ad3e8d28 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 06/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From 04a10a7631ac81ca2bccc96ee4804243d9e52bce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 07/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 9a0628e3d9b26a..e712bfcccd2b64 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=3
+revision=4
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,12 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+CXXFLAGS=-I$XBPS_CROSS_BASE/usr/include/python$py3_ver
+
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From 8ccc9a0a04a4fd4c617d44309c002a74690e7f27 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 10 ++++++++--
1 file changed, 8 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index fc1b22026bad17..b59166ff6e515f 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,10 +1,10 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.12.1
-revision=2
+revision=3
build_style=python3-module
build_helper="numpy"
-hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig"
+hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig hdf5-devel"
makedepends="python3-devel hdf5-devel"
depends="python3-numpy"
short_desc="HDF5 for Python"
@@ -16,6 +16,12 @@ checksum=326d70b53d31baa61f00b8aa5f95c2fcb9621a3ee8365d770c551a13dbbcbfdf
# Tests require unpackaged pytest-mpi
make_check=no
+if [ -n "$CROSS_BUILD" ] && [ "$XBPS_TARGET_WORDSIZE" = "32" ]; then
+ # numpy.complex256 is N/A on 32 bit; it is misdetected if host is 64 bit
+ # we need `DEF COMPLEX256_SUPPORT = False`, this seems the easiest way
+ export CIBW_ARCHS_MACOS=arm64
+fi
+
pre_build() {
# Build in parallel
make_build_args+=" ${makejobs}"
From 85cc66cba5a23834aa846bfba80011e8b84ed81c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 09/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index d8992f76e4f635..bb7fdf9f724262 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.40.2
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
@@ -30,6 +30,7 @@ license="GPL-2.0-only"
homepage="https://qgis.org"
distfiles="https://github.com/qgis/QGIS/archive/final-${version//./_}.tar.gz"
checksum=83d47feceb2e3f9946e5738b6d4bd8092bc97b4836226c45883f4e5afdc50594
+nocross="due to grass"
post_install() {
mv ${DESTDIR}/usr/share/qgis/python ${DESTDIR}/usr/lib/qgis/
From 03323b7f53c5e8e4dd9b8c9ee7d42b95b96243fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From f1ce6fdcb19c96c5336a0dddac2bd21417a89828 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 056d5ed087cf3a..6964c221b92f8f 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.3.1
-revision=2
+revision=3
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
@@ -19,7 +19,7 @@ configure_args="-DBUILD_SHARED_LIBS=ON -DVTK_FORBID_DOWNLOADS=ON
# vtk forks libharu, bumps to v2.4.0, and requires libharu>=2.4.0
makedepends="zlib-devel freetype-devel liblz4-devel expat-devel MesaLib-devel
libXt-devel libjpeg-turbo-devel tiff-devel hdf5-devel netcdf-devel
- libxml2-devel jsoncpp-devel openmpi-devel libogg-devel libtheora-devel
+ libxml2-devel jsoncpp-devel libogg-devel libtheora-devel
eigen double-conversion-devel glew-devel pugixml-devel sqlite-devel
gl2ps-devel proj-devel python3-devel json-c++ fmt-devel"
short_desc="System for 3D computer graphics, image processing, and visualization"
@@ -28,6 +28,14 @@ license="BSD-3-Clause"
homepage="https://www.vtk.org"
distfiles="https://www.vtk.org/files/release/${version:0:3}/VTK-${version}.tar.gz"
checksum=8354ec084ea0d2dc3d23dbe4243823c4bfc270382d0ce8d658939fd50061cab8
+nocross="It seems to need vtk compile tools for the host"
+
+case "$XBPS_TARGET_MACHINE" in
+ # List of supported architectures copied from openmpi.
+ x86_64*|aarch64*|ppc64*|riscv64*)
+ makedepends+=" openmpi-devel"
+ ;;
+esac
if [ "$XBPS_TARGET_LIBC" = "musl" ]; then
makedepends+=" libexecinfo-devel"
From dbe7003d1dc2687f8a34eb960a802ba8fb44d96c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 12/12] octave: update to 9.4.0.
---
srcpkgs/octave/template | 11 +++--------
1 file changed, 3 insertions(+), 8 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index 12c9eb50fc4fe9..2ccd93afee955d 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,6 +1,6 @@
# Template file for 'octave'
pkgname=octave
-version=9.3.0
+version=9.4.0
revision=1
build_style=gnu-configure
build_helper=qmake6
@@ -8,7 +8,7 @@ configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config qt6-base qt6-tools"
makedepends="pcre2-devel readline-devel libSM-devel libltdl-devel lcms2-devel
glpk-devel SuiteSparse-devel rapidjson arpack-ng-devel libsndfile-devel
- portaudio-devel libcurl-devel fftw-devel libgraphicsmagick-devel
+ portaudio-devel libcurl-devel fftw-devel hdf5-devel libgraphicsmagick-devel
qt6-base-devel qt6-tools-devel qt6-qt5compat-devel qt6-plugin-sqlite
qscintilla-qt6-devel glu-devel fltk-devel fontconfig-devel freetype-devel
gl2ps-devel libgomp-devel libqhull-devel zlib-devel"
@@ -20,7 +20,7 @@ license="GPL-3.0-or-later"
homepage="https://octave.org/"
changelog="http://hg.savannah.gnu.org/hgweb/octave/raw-file/default/etc/NEWS.${version%%.*}.md"
distfiles="${GNU_SITE}/octave/octave-${version}.tar.gz"
-checksum=809fa39a7acc84815bf4dc4d2d7e6b228ce75a07f3b2413f3313aa8e0aaa3287
+checksum=da9481205bfa717660b7d4a16732d8b2d58aadceab4993d41242a8e2848ea6c1
# Use OpenBLAS on platforms where it is available and fallback to regular BLAS
# on all others.
@@ -35,11 +35,6 @@ case "$XBPS_TARGET_MACHINE" in
;;
esac
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- makedepends+=" hdf5-devel"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] [WIP] hdf5: update to 1.14.4.3, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (8 preceding siblings ...)
2025-02-12 0:40 ` [PR PATCH] [Updated] " tornaria
@ 2025-02-12 3:02 ` tornaria
2025-02-12 15:36 ` hdf5: update to 1.14.4.6, " tornaria
` (7 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2025-02-12 3:02 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1742 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
[WIP] hdf5: update to 1.14.4.3, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **octave: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **python3-tables: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 26974 bytes --]
From 75062533186c9165a2a5e18846fc0698a81e4858 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.6, fix cross.
---
common/shlibs | 12 ++++-----
...68f4091f1c35f621d2acdeadd34db6756976.patch | 24 ++++++++++++++++++
.../patches/workaround-broken-test-i686.patch | 13 ++++++++++
srcpkgs/hdf5/template | 25 +++++++++++++------
4 files changed, 60 insertions(+), 14 deletions(-)
create mode 100644 srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
create mode 100644 srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
diff --git a/common/shlibs b/common/shlibs
index cc24170f5ec2f7..ddaafb61f88d21 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2648,12 +2648,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.6_1
+libhdf5.so.310 hdf5-1.14.6_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.6_1
+libhdf5_cpp.so.310 hdf5-1.14.6_1
+libhdf5hl_fortran.so.310 hdf5-1.14.6_1
+libhdf5_fortran.so.310 hdf5-1.14.6_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch b/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
new file mode 100644
index 00000000000000..580c94d353c287
--- /dev/null
+++ b/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
@@ -0,0 +1,24 @@
+Fix for 32 bit, see: https://github.com/HDFGroup/hdf5/issues/4916
+
+From 0af668f4091f1c35f621d2acdeadd34db6756976 Mon Sep 17 00:00:00 2001
+From: Orion Poplawski <orion@nwra.com>
+Date: Fri, 4 Oct 2024 13:33:15 -0600
+Subject: [PATCH] Re-add call to AC_CHECK_SIZEOF([__float128]). Fixes #4916.
+ (#4924)
+
+---
+ configure.ac | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/configure.ac b/configure.ac
+index af6c974a2a0..c5bfe4276af 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -854,6 +854,7 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
+ if test "$MY_FLT128_DIG" -gt "$MY_LDBL_DIG" ; then
+ AC_MSG_RESULT([yes])
+ AC_DEFINE([HAVE_FLOAT128], [1], [Determine if __float128 will be used in the Fortran wrappers])
++ AC_CHECK_SIZEOF([__float128])
+ else
+ ## Can't use __float128, but write an undef line anyway
+ AC_MSG_RESULT([no])
diff --git a/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch b/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
new file mode 100644
index 00000000000000..1246996c447e4f
--- /dev/null
+++ b/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
@@ -0,0 +1,13 @@
+This test is broken on i686, see: https://github.com/HDFGroup/hdf5/issues/4926
+
+--- a/fortran/test/tH5R.F90
++++ b/fortran/test/tH5R.F90
+@@ -668,7 +668,7 @@
+ CALL verify("h5rget_obj_name_f", TRIM(buf_big), "/"//groupname1, total_error)
+
+ ! getting path to dataset
+- CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)), "", error, name_len=buf_size )
++ CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)), "A long string is needed here", error, name_len=buf_size )
+ CALL check("H5Rget_name_f", error, total_error)
+ CALL verify("H5Rget_name_f2", INT(buf_size),LEN("/"//groupname1//"/"//groupname2),total_error)
+
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index a2ea9fcd797639..787227ad42ae85 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,31 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.11
+version=1.14.6
revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl autoconf"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://github.com/HDFGroup/hdf5/archive/hdf5-${version//./_}.tar.gz"
-checksum=4ef6375fc7d8c54dcd66e9bc35a7a3580d33cd8878bdf21ad1eb388a43863159
-nocross="https://web.archive.org/web/20230924050239/https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+changelog="https://github.com/HDFGroup/hdf5/releases"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=09ee1c671a87401a5201c06106650f62badeea5a3b3941e9b1e2e1e08317357f
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
+
+pre_configure() {
+ autoconf
+}
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From affb25283e27eff28e6da5c8993228c64a39a9ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From 421f555a53725bd450a09058ce2180e51a8bfcc7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..9e4f38f91e2bad 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/flann-lib/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From dd8a011bd7169814f33d4374f641f2b5cfbe9206 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 11 Feb 2025 21:29:29 -0300
Subject: [PATCH 04/12] med: rebuild for hdf5
---
srcpkgs/med/patches/hdf5-1.14.patch | 99 ++++++++++++++++++++++++++
srcpkgs/med/patches/hdf5-version.patch | 17 +++++
srcpkgs/med/template | 3 +-
3 files changed, 118 insertions(+), 1 deletion(-)
create mode 100644 srcpkgs/med/patches/hdf5-1.14.patch
create mode 100644 srcpkgs/med/patches/hdf5-version.patch
diff --git a/srcpkgs/med/patches/hdf5-1.14.patch b/srcpkgs/med/patches/hdf5-1.14.patch
new file mode 100644
index 00000000000000..4d72add6b9fce9
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-1.14.patch
@@ -0,0 +1,99 @@
+https://salsa.debian.org/science-team/med-fichier/-/blob/master/debian/patches/hdf5-1.14.patch
+
+Index: med-fichier/config/med_check_hdf5.m4
+===================================================================
+--- med-fichier.orig/config/med_check_hdf5.m4
++++ med-fichier/config/med_check_hdf5.m4
+@@ -134,12 +134,6 @@ AC_REQUIRE([AC_PROG_GREP])
+ H5_VER_MINOR=` grep '#define *H5_VERS_MINOR' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_MINOR[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ H5_VER_RELEASE=`grep '#define *H5_VERS_RELEASE' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_RELEASE[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ HDF5_VERSION=` expr 10000 \* ${H5_VER_MAJOR} + 100 \* ${H5_VER_MINOR} + ${H5_VER_RELEASE} `
+- test "0${HDF5_VERSION}" -gt "11100" || test "0${HDF5_VERSION}" -lt "11002" && AC_MSG_ERROR([
+-This HDF5 version ${H5_VER_MAJOR}.${H5_VER_MINOR}.${H5_VER_RELEASE} must not be used with med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE}.
+-The HDF5 library version used by med-fichier${MED_NUM_MAJEUR}.y.z MUST NOT be > 1.10 and have to be at least HDF${HDF_VERSION_REF}.
+-DO NOT TRY TO COMPILE med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE} version with an HDF5 library which would generate an hdf5 file not compliant with HDF5-${HDF_VERSION_MAJOR_REF}.${HDF_VERSION_MINOR_REF}.z library.
+-This would BREAK med-fichier compatibility between files with the same revision number !
+- ])
+ else
+ ## In case user explicitly ask to not use hdf5 !
+ AC_MSG_WARN([Can't compile MED without hdf5])
+Index: med-fichier/src/ci/MEDfileCompatibility.c
+===================================================================
+--- med-fichier.orig/src/ci/MEDfileCompatibility.c
++++ med-fichier/src/ci/MEDfileCompatibility.c
+@@ -15,7 +15,6 @@
+ * along with MED. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+-
+ #include <med.h>
+ #include <med_config.h>
+ #include <med_outils.h>
+@@ -71,7 +70,7 @@ MEDfileCompatibility(const char* const f
+ _hversionMMR=10000*_hmajeur+100*_hmineur+_hrelease;
+ /* ISCRUTE(_hversionMMR); */
+ /* ISCRUTE(HDF_VERSION_NUM_REF); */
+- if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur == HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
++ if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur >= HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
+
+ /* TODO : Vérifier si la version mineure HDF du fichier est supérieure
+ à la version mineure de la bibliothèque HDF utilisée :
+@@ -114,8 +113,8 @@ MEDfileCompatibility(const char* const f
+ #error "Don't forget to update the test version here when you change the major version of the library !"
+ #endif
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
+-#error "Cf. _MEDfileCreate ..."
++#warning "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
++#warning "Cf. _MEDfileCreate ..."
+ #endif
+
+ SORTIE:
+Index: med-fichier/src/hdfi/_MEDfileCreate.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileCreate.c
++++ med-fichier/src/hdfi/_MEDfileCreate.c
+@@ -132,7 +132,7 @@ med_idt _MEDfileCreate(const char * cons
+ {
+ case 0: _release = MED_40_LATEST_RELEASE; break;
+ #if (MED_NUM_MINEUR == 0) && (MED_NUM_RELEASE > 1)
+-#error "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
++#warning "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
+ #endif
+ /* case 1: _release = 0; break; */
+ /* case 2: _release = 1; break; */
+@@ -160,7 +160,7 @@ med_idt _MEDfileCreate(const char * cons
+ * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18 ) ) {
+Index: med-fichier/src/hdfi/_MEDfileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileOpen.c
++++ med-fichier/src/hdfi/_MEDfileOpen.c
+@@ -73,7 +73,7 @@ med_idt _MEDfileOpen(const char * const
+ • The creation order tracking property, H5P_CRT_ORDER_TRACKED, has been set in the group creation property list (see H5Pset_link_creation_order).
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ /* L'avantage de bloquer le modèle interne HDF5
+ est que l'on peut modifier des fichiers med de différentes versions majeures de fichiers.
+Index: med-fichier/src/hdfi/_MEDmemFileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDmemFileOpen.c
++++ med-fichier/src/hdfi/_MEDmemFileOpen.c
+@@ -435,7 +435,7 @@ med_idt _MEDmemFileOpen(const char * con
+ }
+
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18) ) {
+ MED_ERR_(_fid,MED_ERR_INIT,MED_ERR_PROPERTY,MED_ERR_FILEVERSION_MSG);
diff --git a/srcpkgs/med/patches/hdf5-version.patch b/srcpkgs/med/patches/hdf5-version.patch
new file mode 100644
index 00000000000000..36db2c6689906e
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-version.patch
@@ -0,0 +1,17 @@
+Don't complain on hdf5, it works with hdf5 1.14 using `-DH5_USE_110_API=1`
+
+--- a/config/cmake_files/medMacros.cmake
++++ b/config/cmake_files/medMacros.cmake
+@@ -447,9 +447,9 @@
+ ##
+ ## Requires 1.10.x version
+ ##
+- IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
+- MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
+- ENDIF()
++ # IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
++ # MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
++ # ENDIF()
+ ##
+ ##
+
diff --git a/srcpkgs/med/template b/srcpkgs/med/template
index cc553adb493e68..85151578d68825 100644
--- a/srcpkgs/med/template
+++ b/srcpkgs/med/template
@@ -14,7 +14,8 @@ homepage="https://www.salome-platform.org"
distfiles="https://github.com/chennes/med/archive/v${version}.tar.gz"
checksum=ee8b3b6d46bfee25c1d289308b16c7f248d1339161fd5448339382125e6119ad
-nocross="hdf5 is nocross"
+# uses hdf5 old api
+CFLAGS+=" -DH5_USE_110_API=1"
post_extract() {
# The py-compile helper uses the imp module, removed in Python 3.12;
From 88ecdb0317a89a8648a30c4b4949071fff357e97 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 05/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From 4b12ea60fd53d044aa905468dafc14924ea28809 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 06/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From 8362d8009ef2ae4e1c6521b1a718f9f0cd351619 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 07/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 9a0628e3d9b26a..e712bfcccd2b64 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=3
+revision=4
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,12 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+CXXFLAGS=-I$XBPS_CROSS_BASE/usr/include/python$py3_ver
+
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From d6cf75eec4cd50a173d4c4869dded1e880581aa2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index fc1b22026bad17..e9f14fdcb9ff06 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,10 +1,10 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.12.1
-revision=2
+revision=3
build_style=python3-module
build_helper="numpy"
-hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig"
+hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig hdf5-devel"
makedepends="python3-devel hdf5-devel"
depends="python3-numpy"
short_desc="HDF5 for Python"
@@ -16,6 +16,14 @@ checksum=326d70b53d31baa61f00b8aa5f95c2fcb9621a3ee8365d770c551a13dbbcbfdf
# Tests require unpackaged pytest-mpi
make_check=no
+post_patch() {
+ if [ -n "$CROSS_BUILD" ] && [ "$XBPS_TARGET_WORDSIZE" = "32" ]; then
+ # numpy.complex256 is N/A on 32 bit; it is misdetected if host is 64 bit
+ # we need `DEF COMPLEX256_SUPPORT = False`, this seems the easiest way
+ vsed -e 's/{complex256_support}/False/' -i setup_build.py
+ fi
+}
+
pre_build() {
# Build in parallel
make_build_args+=" ${makejobs}"
From d306501463fdc0d8b1c243695a5bfb00b8aafff1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 09/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index d8992f76e4f635..bb7fdf9f724262 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.40.2
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
@@ -30,6 +30,7 @@ license="GPL-2.0-only"
homepage="https://qgis.org"
distfiles="https://github.com/qgis/QGIS/archive/final-${version//./_}.tar.gz"
checksum=83d47feceb2e3f9946e5738b6d4bd8092bc97b4836226c45883f4e5afdc50594
+nocross="due to grass"
post_install() {
mv ${DESTDIR}/usr/share/qgis/python ${DESTDIR}/usr/lib/qgis/
From 65a9d58a3618998be9931fb045ef97c062873849 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From 434ca6b918b0f2803913f339d94fba91970ff96e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 056d5ed087cf3a..6964c221b92f8f 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.3.1
-revision=2
+revision=3
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
@@ -19,7 +19,7 @@ configure_args="-DBUILD_SHARED_LIBS=ON -DVTK_FORBID_DOWNLOADS=ON
# vtk forks libharu, bumps to v2.4.0, and requires libharu>=2.4.0
makedepends="zlib-devel freetype-devel liblz4-devel expat-devel MesaLib-devel
libXt-devel libjpeg-turbo-devel tiff-devel hdf5-devel netcdf-devel
- libxml2-devel jsoncpp-devel openmpi-devel libogg-devel libtheora-devel
+ libxml2-devel jsoncpp-devel libogg-devel libtheora-devel
eigen double-conversion-devel glew-devel pugixml-devel sqlite-devel
gl2ps-devel proj-devel python3-devel json-c++ fmt-devel"
short_desc="System for 3D computer graphics, image processing, and visualization"
@@ -28,6 +28,14 @@ license="BSD-3-Clause"
homepage="https://www.vtk.org"
distfiles="https://www.vtk.org/files/release/${version:0:3}/VTK-${version}.tar.gz"
checksum=8354ec084ea0d2dc3d23dbe4243823c4bfc270382d0ce8d658939fd50061cab8
+nocross="It seems to need vtk compile tools for the host"
+
+case "$XBPS_TARGET_MACHINE" in
+ # List of supported architectures copied from openmpi.
+ x86_64*|aarch64*|ppc64*|riscv64*)
+ makedepends+=" openmpi-devel"
+ ;;
+esac
if [ "$XBPS_TARGET_LIBC" = "musl" ]; then
makedepends+=" libexecinfo-devel"
From 34e31271146519043c3a4391a849dc16a619bddf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 12/12] octave: update to 9.4.0.
---
srcpkgs/octave/template | 11 +++--------
1 file changed, 3 insertions(+), 8 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index 12c9eb50fc4fe9..2ccd93afee955d 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,6 +1,6 @@
# Template file for 'octave'
pkgname=octave
-version=9.3.0
+version=9.4.0
revision=1
build_style=gnu-configure
build_helper=qmake6
@@ -8,7 +8,7 @@ configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config qt6-base qt6-tools"
makedepends="pcre2-devel readline-devel libSM-devel libltdl-devel lcms2-devel
glpk-devel SuiteSparse-devel rapidjson arpack-ng-devel libsndfile-devel
- portaudio-devel libcurl-devel fftw-devel libgraphicsmagick-devel
+ portaudio-devel libcurl-devel fftw-devel hdf5-devel libgraphicsmagick-devel
qt6-base-devel qt6-tools-devel qt6-qt5compat-devel qt6-plugin-sqlite
qscintilla-qt6-devel glu-devel fltk-devel fontconfig-devel freetype-devel
gl2ps-devel libgomp-devel libqhull-devel zlib-devel"
@@ -20,7 +20,7 @@ license="GPL-3.0-or-later"
homepage="https://octave.org/"
changelog="http://hg.savannah.gnu.org/hgweb/octave/raw-file/default/etc/NEWS.${version%%.*}.md"
distfiles="${GNU_SITE}/octave/octave-${version}.tar.gz"
-checksum=809fa39a7acc84815bf4dc4d2d7e6b228ce75a07f3b2413f3313aa8e0aaa3287
+checksum=da9481205bfa717660b7d4a16732d8b2d58aadceab4993d41242a8e2848ea6c1
# Use OpenBLAS on platforms where it is available and fallback to regular BLAS
# on all others.
@@ -35,11 +35,6 @@ case "$XBPS_TARGET_MACHINE" in
;;
esac
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- makedepends+=" hdf5-devel"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: hdf5: update to 1.14.4.6, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (9 preceding siblings ...)
2025-02-12 3:02 ` tornaria
@ 2025-02-12 15:36 ` tornaria
2025-02-26 14:22 ` [PR PATCH] [Updated] " tornaria
` (6 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2025-02-12 15:36 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 372 bytes --]
New comment by tornaria on void-packages repository
https://github.com/void-linux/void-packages/pull/51891#issuecomment-2654081841
Comment:
```
python3-tables-3.7.0_4: broken, unresolvable shlib `libhdf5.so.103'
Transaction aborted due to unresolved shlibs.
Failed to install 'hdf5' and 'python3-tables-3.7.0_4'
```
but `python3-tables` has been removed I think.
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] hdf5: update to 1.14.4.6, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (10 preceding siblings ...)
2025-02-12 15:36 ` hdf5: update to 1.14.4.6, " tornaria
@ 2025-02-26 14:22 ` tornaria
2025-02-26 20:59 ` tornaria
` (5 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2025-02-26 14:22 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1793 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
hdf5: update to 1.14.4.6, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **med: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
- **octave: update to 9.4.0.**
~~Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)~~
Note: **python3-tables** is not rebuilt since it is removed.
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 26974 bytes --]
From 6e7ae61c8f39254fec53c78bb166faf3cd759c4b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.6, fix cross.
---
common/shlibs | 12 ++++-----
...68f4091f1c35f621d2acdeadd34db6756976.patch | 24 ++++++++++++++++++
.../patches/workaround-broken-test-i686.patch | 13 ++++++++++
srcpkgs/hdf5/template | 25 +++++++++++++------
4 files changed, 60 insertions(+), 14 deletions(-)
create mode 100644 srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
create mode 100644 srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
diff --git a/common/shlibs b/common/shlibs
index 659e4a45db77a8..575b959bc70b8d 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2646,12 +2646,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.6_1
+libhdf5.so.310 hdf5-1.14.6_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.6_1
+libhdf5_cpp.so.310 hdf5-1.14.6_1
+libhdf5hl_fortran.so.310 hdf5-1.14.6_1
+libhdf5_fortran.so.310 hdf5-1.14.6_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch b/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
new file mode 100644
index 00000000000000..580c94d353c287
--- /dev/null
+++ b/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
@@ -0,0 +1,24 @@
+Fix for 32 bit, see: https://github.com/HDFGroup/hdf5/issues/4916
+
+From 0af668f4091f1c35f621d2acdeadd34db6756976 Mon Sep 17 00:00:00 2001
+From: Orion Poplawski <orion@nwra.com>
+Date: Fri, 4 Oct 2024 13:33:15 -0600
+Subject: [PATCH] Re-add call to AC_CHECK_SIZEOF([__float128]). Fixes #4916.
+ (#4924)
+
+---
+ configure.ac | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/configure.ac b/configure.ac
+index af6c974a2a0..c5bfe4276af 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -854,6 +854,7 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
+ if test "$MY_FLT128_DIG" -gt "$MY_LDBL_DIG" ; then
+ AC_MSG_RESULT([yes])
+ AC_DEFINE([HAVE_FLOAT128], [1], [Determine if __float128 will be used in the Fortran wrappers])
++ AC_CHECK_SIZEOF([__float128])
+ else
+ ## Can't use __float128, but write an undef line anyway
+ AC_MSG_RESULT([no])
diff --git a/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch b/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
new file mode 100644
index 00000000000000..1246996c447e4f
--- /dev/null
+++ b/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
@@ -0,0 +1,13 @@
+This test is broken on i686, see: https://github.com/HDFGroup/hdf5/issues/4926
+
+--- a/fortran/test/tH5R.F90
++++ b/fortran/test/tH5R.F90
+@@ -668,7 +668,7 @@
+ CALL verify("h5rget_obj_name_f", TRIM(buf_big), "/"//groupname1, total_error)
+
+ ! getting path to dataset
+- CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)), "", error, name_len=buf_size )
++ CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)), "A long string is needed here", error, name_len=buf_size )
+ CALL check("H5Rget_name_f", error, total_error)
+ CALL verify("H5Rget_name_f2", INT(buf_size),LEN("/"//groupname1//"/"//groupname2),total_error)
+
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index a2ea9fcd797639..787227ad42ae85 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,31 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.11
+version=1.14.6
revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl autoconf"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://github.com/HDFGroup/hdf5/archive/hdf5-${version//./_}.tar.gz"
-checksum=4ef6375fc7d8c54dcd66e9bc35a7a3580d33cd8878bdf21ad1eb388a43863159
-nocross="https://web.archive.org/web/20230924050239/https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+changelog="https://github.com/HDFGroup/hdf5/releases"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=09ee1c671a87401a5201c06106650f62badeea5a3b3941e9b1e2e1e08317357f
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
+
+pre_configure() {
+ autoconf
+}
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From 435a903d9dac230a26d3ac36dc52a701377645b2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From cd5d37c2eb4d13cf8fe5280c9d8fdcdf699bfcf3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..9e4f38f91e2bad 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/flann-lib/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From 946902e6091a47f06ee4c746adb29bfa7ebe9e6d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 11 Feb 2025 21:29:29 -0300
Subject: [PATCH 04/12] med: rebuild for hdf5
---
srcpkgs/med/patches/hdf5-1.14.patch | 99 ++++++++++++++++++++++++++
srcpkgs/med/patches/hdf5-version.patch | 17 +++++
srcpkgs/med/template | 3 +-
3 files changed, 118 insertions(+), 1 deletion(-)
create mode 100644 srcpkgs/med/patches/hdf5-1.14.patch
create mode 100644 srcpkgs/med/patches/hdf5-version.patch
diff --git a/srcpkgs/med/patches/hdf5-1.14.patch b/srcpkgs/med/patches/hdf5-1.14.patch
new file mode 100644
index 00000000000000..4d72add6b9fce9
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-1.14.patch
@@ -0,0 +1,99 @@
+https://salsa.debian.org/science-team/med-fichier/-/blob/master/debian/patches/hdf5-1.14.patch
+
+Index: med-fichier/config/med_check_hdf5.m4
+===================================================================
+--- med-fichier.orig/config/med_check_hdf5.m4
++++ med-fichier/config/med_check_hdf5.m4
+@@ -134,12 +134,6 @@ AC_REQUIRE([AC_PROG_GREP])
+ H5_VER_MINOR=` grep '#define *H5_VERS_MINOR' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_MINOR[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ H5_VER_RELEASE=`grep '#define *H5_VERS_RELEASE' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_RELEASE[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ HDF5_VERSION=` expr 10000 \* ${H5_VER_MAJOR} + 100 \* ${H5_VER_MINOR} + ${H5_VER_RELEASE} `
+- test "0${HDF5_VERSION}" -gt "11100" || test "0${HDF5_VERSION}" -lt "11002" && AC_MSG_ERROR([
+-This HDF5 version ${H5_VER_MAJOR}.${H5_VER_MINOR}.${H5_VER_RELEASE} must not be used with med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE}.
+-The HDF5 library version used by med-fichier${MED_NUM_MAJEUR}.y.z MUST NOT be > 1.10 and have to be at least HDF${HDF_VERSION_REF}.
+-DO NOT TRY TO COMPILE med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE} version with an HDF5 library which would generate an hdf5 file not compliant with HDF5-${HDF_VERSION_MAJOR_REF}.${HDF_VERSION_MINOR_REF}.z library.
+-This would BREAK med-fichier compatibility between files with the same revision number !
+- ])
+ else
+ ## In case user explicitly ask to not use hdf5 !
+ AC_MSG_WARN([Can't compile MED without hdf5])
+Index: med-fichier/src/ci/MEDfileCompatibility.c
+===================================================================
+--- med-fichier.orig/src/ci/MEDfileCompatibility.c
++++ med-fichier/src/ci/MEDfileCompatibility.c
+@@ -15,7 +15,6 @@
+ * along with MED. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+-
+ #include <med.h>
+ #include <med_config.h>
+ #include <med_outils.h>
+@@ -71,7 +70,7 @@ MEDfileCompatibility(const char* const f
+ _hversionMMR=10000*_hmajeur+100*_hmineur+_hrelease;
+ /* ISCRUTE(_hversionMMR); */
+ /* ISCRUTE(HDF_VERSION_NUM_REF); */
+- if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur == HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
++ if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur >= HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
+
+ /* TODO : Vérifier si la version mineure HDF du fichier est supérieure
+ à la version mineure de la bibliothèque HDF utilisée :
+@@ -114,8 +113,8 @@ MEDfileCompatibility(const char* const f
+ #error "Don't forget to update the test version here when you change the major version of the library !"
+ #endif
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
+-#error "Cf. _MEDfileCreate ..."
++#warning "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
++#warning "Cf. _MEDfileCreate ..."
+ #endif
+
+ SORTIE:
+Index: med-fichier/src/hdfi/_MEDfileCreate.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileCreate.c
++++ med-fichier/src/hdfi/_MEDfileCreate.c
+@@ -132,7 +132,7 @@ med_idt _MEDfileCreate(const char * cons
+ {
+ case 0: _release = MED_40_LATEST_RELEASE; break;
+ #if (MED_NUM_MINEUR == 0) && (MED_NUM_RELEASE > 1)
+-#error "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
++#warning "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
+ #endif
+ /* case 1: _release = 0; break; */
+ /* case 2: _release = 1; break; */
+@@ -160,7 +160,7 @@ med_idt _MEDfileCreate(const char * cons
+ * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18 ) ) {
+Index: med-fichier/src/hdfi/_MEDfileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileOpen.c
++++ med-fichier/src/hdfi/_MEDfileOpen.c
+@@ -73,7 +73,7 @@ med_idt _MEDfileOpen(const char * const
+ • The creation order tracking property, H5P_CRT_ORDER_TRACKED, has been set in the group creation property list (see H5Pset_link_creation_order).
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ /* L'avantage de bloquer le modèle interne HDF5
+ est que l'on peut modifier des fichiers med de différentes versions majeures de fichiers.
+Index: med-fichier/src/hdfi/_MEDmemFileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDmemFileOpen.c
++++ med-fichier/src/hdfi/_MEDmemFileOpen.c
+@@ -435,7 +435,7 @@ med_idt _MEDmemFileOpen(const char * con
+ }
+
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18) ) {
+ MED_ERR_(_fid,MED_ERR_INIT,MED_ERR_PROPERTY,MED_ERR_FILEVERSION_MSG);
diff --git a/srcpkgs/med/patches/hdf5-version.patch b/srcpkgs/med/patches/hdf5-version.patch
new file mode 100644
index 00000000000000..36db2c6689906e
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-version.patch
@@ -0,0 +1,17 @@
+Don't complain on hdf5, it works with hdf5 1.14 using `-DH5_USE_110_API=1`
+
+--- a/config/cmake_files/medMacros.cmake
++++ b/config/cmake_files/medMacros.cmake
+@@ -447,9 +447,9 @@
+ ##
+ ## Requires 1.10.x version
+ ##
+- IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
+- MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
+- ENDIF()
++ # IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
++ # MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
++ # ENDIF()
+ ##
+ ##
+
diff --git a/srcpkgs/med/template b/srcpkgs/med/template
index cc553adb493e68..85151578d68825 100644
--- a/srcpkgs/med/template
+++ b/srcpkgs/med/template
@@ -14,7 +14,8 @@ homepage="https://www.salome-platform.org"
distfiles="https://github.com/chennes/med/archive/v${version}.tar.gz"
checksum=ee8b3b6d46bfee25c1d289308b16c7f248d1339161fd5448339382125e6119ad
-nocross="hdf5 is nocross"
+# uses hdf5 old api
+CFLAGS+=" -DH5_USE_110_API=1"
post_extract() {
# The py-compile helper uses the imp module, removed in Python 3.12;
From 3097c8b6f90c56b36fbe54922a37cf3757edf28e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 05/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From 8d7de78752ba3adb527c0a545ba2dc354f48d86c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 06/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From 1904a6e9c9ad4740dc92bf114d9c28059e946b9f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 07/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 9a0628e3d9b26a..e712bfcccd2b64 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=3
+revision=4
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,12 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+CXXFLAGS=-I$XBPS_CROSS_BASE/usr/include/python$py3_ver
+
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From 782fc16902c3828ddb0b54220477c37939f400c5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index c95ea6d7bee775..1928815fe79f9c 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,10 +1,10 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.13.0
-revision=1
+revision=2
build_style=python3-module
build_helper="numpy"
-hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig"
+hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig hdf5-devel"
makedepends="python3-devel hdf5-devel"
depends="python3-numpy"
short_desc="HDF5 for Python"
@@ -16,6 +16,14 @@ checksum=1870e46518720023da85d0895a1960ff2ce398c5671eac3b1a41ec696b7105c3
# Tests require unpackaged pytest-mpi
make_check=no
+post_patch() {
+ if [ -n "$CROSS_BUILD" ] && [ "$XBPS_TARGET_WORDSIZE" = "32" ]; then
+ # numpy.complex256 is N/A on 32 bit; it is misdetected if host is 64 bit
+ # we need `DEF COMPLEX256_SUPPORT = False`, this seems the easiest way
+ vsed -e 's/{complex256_support}/False/' -i setup_build.py
+ fi
+}
+
pre_build() {
# Build in parallel
make_build_args+=" ${makejobs}"
From e603dafc33c847495f8d1f3e56db158218193391 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 09/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index d8992f76e4f635..bb7fdf9f724262 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.40.2
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
@@ -30,6 +30,7 @@ license="GPL-2.0-only"
homepage="https://qgis.org"
distfiles="https://github.com/qgis/QGIS/archive/final-${version//./_}.tar.gz"
checksum=83d47feceb2e3f9946e5738b6d4bd8092bc97b4836226c45883f4e5afdc50594
+nocross="due to grass"
post_install() {
mv ${DESTDIR}/usr/share/qgis/python ${DESTDIR}/usr/lib/qgis/
From b0662853ed3e4baa14f31fd75af473ab127dd667 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From 0f44b8da13c38fd7364531e23cc1f2b6c45fa8bf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 056d5ed087cf3a..6964c221b92f8f 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.3.1
-revision=2
+revision=3
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
@@ -19,7 +19,7 @@ configure_args="-DBUILD_SHARED_LIBS=ON -DVTK_FORBID_DOWNLOADS=ON
# vtk forks libharu, bumps to v2.4.0, and requires libharu>=2.4.0
makedepends="zlib-devel freetype-devel liblz4-devel expat-devel MesaLib-devel
libXt-devel libjpeg-turbo-devel tiff-devel hdf5-devel netcdf-devel
- libxml2-devel jsoncpp-devel openmpi-devel libogg-devel libtheora-devel
+ libxml2-devel jsoncpp-devel libogg-devel libtheora-devel
eigen double-conversion-devel glew-devel pugixml-devel sqlite-devel
gl2ps-devel proj-devel python3-devel json-c++ fmt-devel"
short_desc="System for 3D computer graphics, image processing, and visualization"
@@ -28,6 +28,14 @@ license="BSD-3-Clause"
homepage="https://www.vtk.org"
distfiles="https://www.vtk.org/files/release/${version:0:3}/VTK-${version}.tar.gz"
checksum=8354ec084ea0d2dc3d23dbe4243823c4bfc270382d0ce8d658939fd50061cab8
+nocross="It seems to need vtk compile tools for the host"
+
+case "$XBPS_TARGET_MACHINE" in
+ # List of supported architectures copied from openmpi.
+ x86_64*|aarch64*|ppc64*|riscv64*)
+ makedepends+=" openmpi-devel"
+ ;;
+esac
if [ "$XBPS_TARGET_LIBC" = "musl" ]; then
makedepends+=" libexecinfo-devel"
From 678ef4d2ce66ae60e516c2acea9221eef68acf8e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 12/12] octave: update to 9.4.0.
---
srcpkgs/octave/template | 11 +++--------
1 file changed, 3 insertions(+), 8 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index 12c9eb50fc4fe9..2ccd93afee955d 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,6 +1,6 @@
# Template file for 'octave'
pkgname=octave
-version=9.3.0
+version=9.4.0
revision=1
build_style=gnu-configure
build_helper=qmake6
@@ -8,7 +8,7 @@ configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config qt6-base qt6-tools"
makedepends="pcre2-devel readline-devel libSM-devel libltdl-devel lcms2-devel
glpk-devel SuiteSparse-devel rapidjson arpack-ng-devel libsndfile-devel
- portaudio-devel libcurl-devel fftw-devel libgraphicsmagick-devel
+ portaudio-devel libcurl-devel fftw-devel hdf5-devel libgraphicsmagick-devel
qt6-base-devel qt6-tools-devel qt6-qt5compat-devel qt6-plugin-sqlite
qscintilla-qt6-devel glu-devel fltk-devel fontconfig-devel freetype-devel
gl2ps-devel libgomp-devel libqhull-devel zlib-devel"
@@ -20,7 +20,7 @@ license="GPL-3.0-or-later"
homepage="https://octave.org/"
changelog="http://hg.savannah.gnu.org/hgweb/octave/raw-file/default/etc/NEWS.${version%%.*}.md"
distfiles="${GNU_SITE}/octave/octave-${version}.tar.gz"
-checksum=809fa39a7acc84815bf4dc4d2d7e6b228ce75a07f3b2413f3313aa8e0aaa3287
+checksum=da9481205bfa717660b7d4a16732d8b2d58aadceab4993d41242a8e2848ea6c1
# Use OpenBLAS on platforms where it is available and fallback to regular BLAS
# on all others.
@@ -35,11 +35,6 @@ case "$XBPS_TARGET_MACHINE" in
;;
esac
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- makedepends+=" hdf5-devel"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: hdf5: update to 1.14.4.6, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (11 preceding siblings ...)
2025-02-26 14:22 ` [PR PATCH] [Updated] " tornaria
@ 2025-02-26 20:59 ` tornaria
2025-03-07 1:48 ` tornaria
` (4 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2025-02-26 20:59 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 349 bytes --]
New comment by tornaria on void-packages repository
https://github.com/void-linux/void-packages/pull/51891#issuecomment-2686183335
Comment:
I rebased (since `python3-h5py` was updated) and all checks passed again, except for the final
```
Transaction aborted due to unresolved shlibs.
Failed to install 'hdf5' and 'python3-tables-3.7.0_4'
```
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: hdf5: update to 1.14.4.6, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (12 preceding siblings ...)
2025-02-26 20:59 ` tornaria
@ 2025-03-07 1:48 ` tornaria
2025-03-07 10:55 ` ahesford
` (3 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2025-03-07 1:48 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 595 bytes --]
New comment by tornaria on void-packages repository
https://github.com/void-linux/void-packages/pull/51891#issuecomment-2705329093
Comment:
@ahesford any thoughts on what to do here?
```
Transaction aborted due to unresolved shlibs.
Failed to install 'hdf5' and 'python3-tables-3.7.0_4'
```
is the only thing holding this. I don't think keeping this package in the repo is good for anything since it's built for python 3.12. An interested party can go an package a new version of python-tables; I can even volunteer to create a template *if there's someone using it to tell me it works*.
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: hdf5: update to 1.14.4.6, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (13 preceding siblings ...)
2025-03-07 1:48 ` tornaria
@ 2025-03-07 10:55 ` ahesford
2025-03-07 15:01 ` [PR PATCH] [Updated] " tornaria
` (2 subsequent siblings)
17 siblings, 0 replies; 19+ messages in thread
From: ahesford @ 2025-03-07 10:55 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 231 bytes --]
New comment by ahesford on void-packages repository
https://github.com/void-linux/void-packages/pull/51891#issuecomment-2706146528
Comment:
I've asked for removal of `python3-tables`, so the dependent problem should be resolved.
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] hdf5: update to 1.14.4.6, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (14 preceding siblings ...)
2025-03-07 10:55 ` ahesford
@ 2025-03-07 15:01 ` tornaria
2025-03-07 19:51 ` tornaria
2025-03-08 13:47 ` [PR PATCH] [Merged]: " ahesford
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2025-03-07 15:01 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1793 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
hdf5: update to 1.14.4.6, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **med: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
- **octave: update to 9.4.0.**
~~Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)~~
Note: **python3-tables** is not rebuilt since it is removed.
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
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Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 26974 bytes --]
From 8e03b89179d322658dfd2d5e6b292b94c66ea7ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.6, fix cross.
---
common/shlibs | 12 ++++-----
...68f4091f1c35f621d2acdeadd34db6756976.patch | 24 ++++++++++++++++++
.../patches/workaround-broken-test-i686.patch | 13 ++++++++++
srcpkgs/hdf5/template | 25 +++++++++++++------
4 files changed, 60 insertions(+), 14 deletions(-)
create mode 100644 srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
create mode 100644 srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
diff --git a/common/shlibs b/common/shlibs
index eab9adbbf5df7f..a6b26f6e9e9318 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2646,12 +2646,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.6_1
+libhdf5.so.310 hdf5-1.14.6_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.6_1
+libhdf5_cpp.so.310 hdf5-1.14.6_1
+libhdf5hl_fortran.so.310 hdf5-1.14.6_1
+libhdf5_fortran.so.310 hdf5-1.14.6_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch b/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
new file mode 100644
index 00000000000000..580c94d353c287
--- /dev/null
+++ b/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
@@ -0,0 +1,24 @@
+Fix for 32 bit, see: https://github.com/HDFGroup/hdf5/issues/4916
+
+From 0af668f4091f1c35f621d2acdeadd34db6756976 Mon Sep 17 00:00:00 2001
+From: Orion Poplawski <orion@nwra.com>
+Date: Fri, 4 Oct 2024 13:33:15 -0600
+Subject: [PATCH] Re-add call to AC_CHECK_SIZEOF([__float128]). Fixes #4916.
+ (#4924)
+
+---
+ configure.ac | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/configure.ac b/configure.ac
+index af6c974a2a0..c5bfe4276af 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -854,6 +854,7 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
+ if test "$MY_FLT128_DIG" -gt "$MY_LDBL_DIG" ; then
+ AC_MSG_RESULT([yes])
+ AC_DEFINE([HAVE_FLOAT128], [1], [Determine if __float128 will be used in the Fortran wrappers])
++ AC_CHECK_SIZEOF([__float128])
+ else
+ ## Can't use __float128, but write an undef line anyway
+ AC_MSG_RESULT([no])
diff --git a/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch b/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
new file mode 100644
index 00000000000000..1246996c447e4f
--- /dev/null
+++ b/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
@@ -0,0 +1,13 @@
+This test is broken on i686, see: https://github.com/HDFGroup/hdf5/issues/4926
+
+--- a/fortran/test/tH5R.F90
++++ b/fortran/test/tH5R.F90
+@@ -668,7 +668,7 @@
+ CALL verify("h5rget_obj_name_f", TRIM(buf_big), "/"//groupname1, total_error)
+
+ ! getting path to dataset
+- CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)), "", error, name_len=buf_size )
++ CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)), "A long string is needed here", error, name_len=buf_size )
+ CALL check("H5Rget_name_f", error, total_error)
+ CALL verify("H5Rget_name_f2", INT(buf_size),LEN("/"//groupname1//"/"//groupname2),total_error)
+
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index a2ea9fcd797639..787227ad42ae85 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,31 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.11
+version=1.14.6
revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl autoconf"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://github.com/HDFGroup/hdf5/archive/hdf5-${version//./_}.tar.gz"
-checksum=4ef6375fc7d8c54dcd66e9bc35a7a3580d33cd8878bdf21ad1eb388a43863159
-nocross="https://web.archive.org/web/20230924050239/https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+changelog="https://github.com/HDFGroup/hdf5/releases"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=09ee1c671a87401a5201c06106650f62badeea5a3b3941e9b1e2e1e08317357f
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
+
+pre_configure() {
+ autoconf
+}
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From 261c7a3bb176c31f236e0a14be499af26069d7b4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From 1e0640efdbb669bbb2786ce88cd66d716ebd052d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..9e4f38f91e2bad 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/flann-lib/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From 3fde463f39cfc94194e0ca81a69fec21226fda2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 11 Feb 2025 21:29:29 -0300
Subject: [PATCH 04/12] med: rebuild for hdf5
---
srcpkgs/med/patches/hdf5-1.14.patch | 99 ++++++++++++++++++++++++++
srcpkgs/med/patches/hdf5-version.patch | 17 +++++
srcpkgs/med/template | 3 +-
3 files changed, 118 insertions(+), 1 deletion(-)
create mode 100644 srcpkgs/med/patches/hdf5-1.14.patch
create mode 100644 srcpkgs/med/patches/hdf5-version.patch
diff --git a/srcpkgs/med/patches/hdf5-1.14.patch b/srcpkgs/med/patches/hdf5-1.14.patch
new file mode 100644
index 00000000000000..4d72add6b9fce9
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-1.14.patch
@@ -0,0 +1,99 @@
+https://salsa.debian.org/science-team/med-fichier/-/blob/master/debian/patches/hdf5-1.14.patch
+
+Index: med-fichier/config/med_check_hdf5.m4
+===================================================================
+--- med-fichier.orig/config/med_check_hdf5.m4
++++ med-fichier/config/med_check_hdf5.m4
+@@ -134,12 +134,6 @@ AC_REQUIRE([AC_PROG_GREP])
+ H5_VER_MINOR=` grep '#define *H5_VERS_MINOR' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_MINOR[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ H5_VER_RELEASE=`grep '#define *H5_VERS_RELEASE' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_RELEASE[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ HDF5_VERSION=` expr 10000 \* ${H5_VER_MAJOR} + 100 \* ${H5_VER_MINOR} + ${H5_VER_RELEASE} `
+- test "0${HDF5_VERSION}" -gt "11100" || test "0${HDF5_VERSION}" -lt "11002" && AC_MSG_ERROR([
+-This HDF5 version ${H5_VER_MAJOR}.${H5_VER_MINOR}.${H5_VER_RELEASE} must not be used with med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE}.
+-The HDF5 library version used by med-fichier${MED_NUM_MAJEUR}.y.z MUST NOT be > 1.10 and have to be at least HDF${HDF_VERSION_REF}.
+-DO NOT TRY TO COMPILE med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE} version with an HDF5 library which would generate an hdf5 file not compliant with HDF5-${HDF_VERSION_MAJOR_REF}.${HDF_VERSION_MINOR_REF}.z library.
+-This would BREAK med-fichier compatibility between files with the same revision number !
+- ])
+ else
+ ## In case user explicitly ask to not use hdf5 !
+ AC_MSG_WARN([Can't compile MED without hdf5])
+Index: med-fichier/src/ci/MEDfileCompatibility.c
+===================================================================
+--- med-fichier.orig/src/ci/MEDfileCompatibility.c
++++ med-fichier/src/ci/MEDfileCompatibility.c
+@@ -15,7 +15,6 @@
+ * along with MED. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+-
+ #include <med.h>
+ #include <med_config.h>
+ #include <med_outils.h>
+@@ -71,7 +70,7 @@ MEDfileCompatibility(const char* const f
+ _hversionMMR=10000*_hmajeur+100*_hmineur+_hrelease;
+ /* ISCRUTE(_hversionMMR); */
+ /* ISCRUTE(HDF_VERSION_NUM_REF); */
+- if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur == HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
++ if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur >= HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
+
+ /* TODO : Vérifier si la version mineure HDF du fichier est supérieure
+ à la version mineure de la bibliothèque HDF utilisée :
+@@ -114,8 +113,8 @@ MEDfileCompatibility(const char* const f
+ #error "Don't forget to update the test version here when you change the major version of the library !"
+ #endif
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
+-#error "Cf. _MEDfileCreate ..."
++#warning "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
++#warning "Cf. _MEDfileCreate ..."
+ #endif
+
+ SORTIE:
+Index: med-fichier/src/hdfi/_MEDfileCreate.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileCreate.c
++++ med-fichier/src/hdfi/_MEDfileCreate.c
+@@ -132,7 +132,7 @@ med_idt _MEDfileCreate(const char * cons
+ {
+ case 0: _release = MED_40_LATEST_RELEASE; break;
+ #if (MED_NUM_MINEUR == 0) && (MED_NUM_RELEASE > 1)
+-#error "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
++#warning "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
+ #endif
+ /* case 1: _release = 0; break; */
+ /* case 2: _release = 1; break; */
+@@ -160,7 +160,7 @@ med_idt _MEDfileCreate(const char * cons
+ * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18 ) ) {
+Index: med-fichier/src/hdfi/_MEDfileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileOpen.c
++++ med-fichier/src/hdfi/_MEDfileOpen.c
+@@ -73,7 +73,7 @@ med_idt _MEDfileOpen(const char * const
+ • The creation order tracking property, H5P_CRT_ORDER_TRACKED, has been set in the group creation property list (see H5Pset_link_creation_order).
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ /* L'avantage de bloquer le modèle interne HDF5
+ est que l'on peut modifier des fichiers med de différentes versions majeures de fichiers.
+Index: med-fichier/src/hdfi/_MEDmemFileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDmemFileOpen.c
++++ med-fichier/src/hdfi/_MEDmemFileOpen.c
+@@ -435,7 +435,7 @@ med_idt _MEDmemFileOpen(const char * con
+ }
+
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18) ) {
+ MED_ERR_(_fid,MED_ERR_INIT,MED_ERR_PROPERTY,MED_ERR_FILEVERSION_MSG);
diff --git a/srcpkgs/med/patches/hdf5-version.patch b/srcpkgs/med/patches/hdf5-version.patch
new file mode 100644
index 00000000000000..36db2c6689906e
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-version.patch
@@ -0,0 +1,17 @@
+Don't complain on hdf5, it works with hdf5 1.14 using `-DH5_USE_110_API=1`
+
+--- a/config/cmake_files/medMacros.cmake
++++ b/config/cmake_files/medMacros.cmake
+@@ -447,9 +447,9 @@
+ ##
+ ## Requires 1.10.x version
+ ##
+- IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
+- MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
+- ENDIF()
++ # IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
++ # MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
++ # ENDIF()
+ ##
+ ##
+
diff --git a/srcpkgs/med/template b/srcpkgs/med/template
index cc553adb493e68..85151578d68825 100644
--- a/srcpkgs/med/template
+++ b/srcpkgs/med/template
@@ -14,7 +14,8 @@ homepage="https://www.salome-platform.org"
distfiles="https://github.com/chennes/med/archive/v${version}.tar.gz"
checksum=ee8b3b6d46bfee25c1d289308b16c7f248d1339161fd5448339382125e6119ad
-nocross="hdf5 is nocross"
+# uses hdf5 old api
+CFLAGS+=" -DH5_USE_110_API=1"
post_extract() {
# The py-compile helper uses the imp module, removed in Python 3.12;
From 8a83f519be855273f7434a4210e2b7372fdf5ce1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 05/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From 8bb310790a30b5b718d722c3597589e9b65ebc73 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 06/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From 66772fc9ff8a172196911f2c23c9458511cba7dd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 07/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 9a0628e3d9b26a..e712bfcccd2b64 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=3
+revision=4
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,12 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+CXXFLAGS=-I$XBPS_CROSS_BASE/usr/include/python$py3_ver
+
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From 22cf8851e3fe932118413d1f1b32f189cc598156 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index c95ea6d7bee775..1928815fe79f9c 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,10 +1,10 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.13.0
-revision=1
+revision=2
build_style=python3-module
build_helper="numpy"
-hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig"
+hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig hdf5-devel"
makedepends="python3-devel hdf5-devel"
depends="python3-numpy"
short_desc="HDF5 for Python"
@@ -16,6 +16,14 @@ checksum=1870e46518720023da85d0895a1960ff2ce398c5671eac3b1a41ec696b7105c3
# Tests require unpackaged pytest-mpi
make_check=no
+post_patch() {
+ if [ -n "$CROSS_BUILD" ] && [ "$XBPS_TARGET_WORDSIZE" = "32" ]; then
+ # numpy.complex256 is N/A on 32 bit; it is misdetected if host is 64 bit
+ # we need `DEF COMPLEX256_SUPPORT = False`, this seems the easiest way
+ vsed -e 's/{complex256_support}/False/' -i setup_build.py
+ fi
+}
+
pre_build() {
# Build in parallel
make_build_args+=" ${makejobs}"
From 891c5c447acae47405fafd73a6fa915683f1d9a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 09/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index d8992f76e4f635..bb7fdf9f724262 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.40.2
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
@@ -30,6 +30,7 @@ license="GPL-2.0-only"
homepage="https://qgis.org"
distfiles="https://github.com/qgis/QGIS/archive/final-${version//./_}.tar.gz"
checksum=83d47feceb2e3f9946e5738b6d4bd8092bc97b4836226c45883f4e5afdc50594
+nocross="due to grass"
post_install() {
mv ${DESTDIR}/usr/share/qgis/python ${DESTDIR}/usr/lib/qgis/
From 6d0bb3cd4a20fad6f1d39f2aa330b925681f1374 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From 9d5f06b7fb3406ebbe8f12db41081738a3f8efbf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 056d5ed087cf3a..6964c221b92f8f 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.3.1
-revision=2
+revision=3
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
@@ -19,7 +19,7 @@ configure_args="-DBUILD_SHARED_LIBS=ON -DVTK_FORBID_DOWNLOADS=ON
# vtk forks libharu, bumps to v2.4.0, and requires libharu>=2.4.0
makedepends="zlib-devel freetype-devel liblz4-devel expat-devel MesaLib-devel
libXt-devel libjpeg-turbo-devel tiff-devel hdf5-devel netcdf-devel
- libxml2-devel jsoncpp-devel openmpi-devel libogg-devel libtheora-devel
+ libxml2-devel jsoncpp-devel libogg-devel libtheora-devel
eigen double-conversion-devel glew-devel pugixml-devel sqlite-devel
gl2ps-devel proj-devel python3-devel json-c++ fmt-devel"
short_desc="System for 3D computer graphics, image processing, and visualization"
@@ -28,6 +28,14 @@ license="BSD-3-Clause"
homepage="https://www.vtk.org"
distfiles="https://www.vtk.org/files/release/${version:0:3}/VTK-${version}.tar.gz"
checksum=8354ec084ea0d2dc3d23dbe4243823c4bfc270382d0ce8d658939fd50061cab8
+nocross="It seems to need vtk compile tools for the host"
+
+case "$XBPS_TARGET_MACHINE" in
+ # List of supported architectures copied from openmpi.
+ x86_64*|aarch64*|ppc64*|riscv64*)
+ makedepends+=" openmpi-devel"
+ ;;
+esac
if [ "$XBPS_TARGET_LIBC" = "musl" ]; then
makedepends+=" libexecinfo-devel"
From 8282481f5eac3a4d0aeffbca95b6b2ce02d51dff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 12/12] octave: update to 9.4.0.
---
srcpkgs/octave/template | 11 +++--------
1 file changed, 3 insertions(+), 8 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index 12c9eb50fc4fe9..2ccd93afee955d 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,6 +1,6 @@
# Template file for 'octave'
pkgname=octave
-version=9.3.0
+version=9.4.0
revision=1
build_style=gnu-configure
build_helper=qmake6
@@ -8,7 +8,7 @@ configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config qt6-base qt6-tools"
makedepends="pcre2-devel readline-devel libSM-devel libltdl-devel lcms2-devel
glpk-devel SuiteSparse-devel rapidjson arpack-ng-devel libsndfile-devel
- portaudio-devel libcurl-devel fftw-devel libgraphicsmagick-devel
+ portaudio-devel libcurl-devel fftw-devel hdf5-devel libgraphicsmagick-devel
qt6-base-devel qt6-tools-devel qt6-qt5compat-devel qt6-plugin-sqlite
qscintilla-qt6-devel glu-devel fltk-devel fontconfig-devel freetype-devel
gl2ps-devel libgomp-devel libqhull-devel zlib-devel"
@@ -20,7 +20,7 @@ license="GPL-3.0-or-later"
homepage="https://octave.org/"
changelog="http://hg.savannah.gnu.org/hgweb/octave/raw-file/default/etc/NEWS.${version%%.*}.md"
distfiles="${GNU_SITE}/octave/octave-${version}.tar.gz"
-checksum=809fa39a7acc84815bf4dc4d2d7e6b228ce75a07f3b2413f3313aa8e0aaa3287
+checksum=da9481205bfa717660b7d4a16732d8b2d58aadceab4993d41242a8e2848ea6c1
# Use OpenBLAS on platforms where it is available and fallback to regular BLAS
# on all others.
@@ -35,11 +35,6 @@ case "$XBPS_TARGET_MACHINE" in
;;
esac
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- makedepends+=" hdf5-devel"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Updated] hdf5: update to 1.14.4.6, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (15 preceding siblings ...)
2025-03-07 15:01 ` [PR PATCH] [Updated] " tornaria
@ 2025-03-07 19:51 ` tornaria
2025-03-08 13:47 ` [PR PATCH] [Merged]: " ahesford
17 siblings, 0 replies; 19+ messages in thread
From: tornaria @ 2025-03-07 19:51 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1793 bytes --]
There is an updated pull request by tornaria against master on the void-packages repository
https://github.com/tornaria/void-packages hdf5
https://github.com/void-linux/void-packages/pull/51891
hdf5: update to 1.14.4.6, fix cross.
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **med: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
- **octave: update to 9.4.0.**
~~Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)~~
Note: **python3-tables** is not rebuilt since it is removed.
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#continuous-integration
and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
A patch file from https://github.com/void-linux/void-packages/pull/51891.patch is attached
[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-hdf5-51891.patch --]
[-- Type: text/x-diff, Size: 26974 bytes --]
From 5a6c436f90bc357c1a254b20aba266230c11d9f8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 22:53:50 -0300
Subject: [PATCH 01/12] hdf5: update to 1.14.6, fix cross.
---
common/shlibs | 12 ++++-----
...68f4091f1c35f621d2acdeadd34db6756976.patch | 24 ++++++++++++++++++
.../patches/workaround-broken-test-i686.patch | 13 ++++++++++
srcpkgs/hdf5/template | 25 +++++++++++++------
4 files changed, 60 insertions(+), 14 deletions(-)
create mode 100644 srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
create mode 100644 srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
diff --git a/common/shlibs b/common/shlibs
index eab9adbbf5df7f..a6b26f6e9e9318 100644
--- a/common/shlibs
+++ b/common/shlibs
@@ -2646,12 +2646,12 @@ libpjsip-ua.so.2 pjproject-2.8_5
libpjsip.so.2 pjproject-2.8_5
libpjsua.so.2 pjproject-2.8_5
libpjsua2.so.2 pjproject-2.8_5
-libhdf5_hl.so.100 hdf5-1.10.1_2
-libhdf5.so.103 hdf5-1.10.4_1
-libhdf5_hl_cpp.so.100 hdf5-1.10.1_2
-libhdf5_cpp.so.103 hdf5-1.10.4_1
-libhdf5hl_fortran.so.100 hdf5-1.10.1_2
-libhdf5_fortran.so.102 hdf5-1.10.5_1
+libhdf5_hl.so.310 hdf5-1.14.6_1
+libhdf5.so.310 hdf5-1.14.6_1
+libhdf5_hl_cpp.so.310 hdf5-1.14.6_1
+libhdf5_cpp.so.310 hdf5-1.14.6_1
+libhdf5hl_fortran.so.310 hdf5-1.14.6_1
+libhdf5_fortran.so.310 hdf5-1.14.6_1
libcryptmount.so.0 libpam-mount-2.15_1
libglob.so.0 libglob-1.0_1
libepub.so.0 ebook-tools-0.2.2_1
diff --git a/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch b/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
new file mode 100644
index 00000000000000..580c94d353c287
--- /dev/null
+++ b/srcpkgs/hdf5/patches/0af668f4091f1c35f621d2acdeadd34db6756976.patch
@@ -0,0 +1,24 @@
+Fix for 32 bit, see: https://github.com/HDFGroup/hdf5/issues/4916
+
+From 0af668f4091f1c35f621d2acdeadd34db6756976 Mon Sep 17 00:00:00 2001
+From: Orion Poplawski <orion@nwra.com>
+Date: Fri, 4 Oct 2024 13:33:15 -0600
+Subject: [PATCH] Re-add call to AC_CHECK_SIZEOF([__float128]). Fixes #4916.
+ (#4924)
+
+---
+ configure.ac | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/configure.ac b/configure.ac
+index af6c974a2a0..c5bfe4276af 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -854,6 +854,7 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
+ if test "$MY_FLT128_DIG" -gt "$MY_LDBL_DIG" ; then
+ AC_MSG_RESULT([yes])
+ AC_DEFINE([HAVE_FLOAT128], [1], [Determine if __float128 will be used in the Fortran wrappers])
++ AC_CHECK_SIZEOF([__float128])
+ else
+ ## Can't use __float128, but write an undef line anyway
+ AC_MSG_RESULT([no])
diff --git a/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch b/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
new file mode 100644
index 00000000000000..1246996c447e4f
--- /dev/null
+++ b/srcpkgs/hdf5/patches/workaround-broken-test-i686.patch
@@ -0,0 +1,13 @@
+This test is broken on i686, see: https://github.com/HDFGroup/hdf5/issues/4926
+
+--- a/fortran/test/tH5R.F90
++++ b/fortran/test/tH5R.F90
+@@ -668,7 +668,7 @@
+ CALL verify("h5rget_obj_name_f", TRIM(buf_big), "/"//groupname1, total_error)
+
+ ! getting path to dataset
+- CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)), "", error, name_len=buf_size )
++ CALL h5rget_obj_name_f(C_LOC(ref_ptr(2)), "A long string is needed here", error, name_len=buf_size )
+ CALL check("H5Rget_name_f", error, total_error)
+ CALL verify("H5Rget_name_f2", INT(buf_size),LEN("/"//groupname1//"/"//groupname2),total_error)
+
diff --git a/srcpkgs/hdf5/template b/srcpkgs/hdf5/template
index a2ea9fcd797639..787227ad42ae85 100644
--- a/srcpkgs/hdf5/template
+++ b/srcpkgs/hdf5/template
@@ -1,22 +1,31 @@
# Template file for 'hdf5'
pkgname=hdf5
-version=1.10.11
+version=1.14.6
revision=1
build_style=gnu-configure
-configure_args="--enable-cxx --enable-fortran"
-hostmakedepends="gcc-fortran"
+configure_args="--enable-cxx"
+hostmakedepends="perl autoconf"
makedepends="zlib-devel"
short_desc="Data model, library, and file format for storing and managing data"
maintainer="pulux <pulux@pf4sh.de>"
license="custom:BSD-3-Clause-LBNL-alike"
-homepage="https://hdfgroup.org"
-distfiles="https://github.com/HDFGroup/hdf5/archive/hdf5-${version//./_}.tar.gz"
-checksum=4ef6375fc7d8c54dcd66e9bc35a7a3580d33cd8878bdf21ad1eb388a43863159
-nocross="https://web.archive.org/web/20230924050239/https://portal.hdfgroup.org/pages/viewpage.action?pageId=48808266"
+homepage="https://www.hdfgroup.org/solutions/hdf5/"
+changelog="https://github.com/HDFGroup/hdf5/releases"
+distfiles="https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${version}.tar.gz"
+checksum=09ee1c671a87401a5201c06106650f62badeea5a3b3941e9b1e2e1e08317357f
+
+if [ -z "$CROSS_BUILD" ]; then
+ # fortran support needs to run programs to configure
+ configure_args+=" --enable-fortran"
+ hostmakedepends+=" gcc-fortran"
+fi
+
+pre_configure() {
+ autoconf
+}
post_install() {
vlicense COPYING
- rm -rf ${DESTDIR}/usr/lib/libdynlib*.so
}
hdf5-devel_package() {
From 0945d768ded9e5d7f16b92ccf8f4ff67d6f33cb6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:02 -0300
Subject: [PATCH 02/12] Field3D: rebuild for hdf5
---
srcpkgs/Field3D/template | 5 ++++-
1 file changed, 4 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/Field3D/template b/srcpkgs/Field3D/template
index a3844448abef37..f0627cce5aad23 100644
--- a/srcpkgs/Field3D/template
+++ b/srcpkgs/Field3D/template
@@ -1,7 +1,7 @@
# Template file for 'Field3D'
pkgname=Field3D
version=1.7.3
-revision=9
+revision=10
build_style=cmake
makedepends="boost-devel hdf5-devel imath-devel libopenexr-devel"
short_desc="Library for storing voxel data on disk and in memory"
@@ -11,6 +11,9 @@ homepage="https://github.com/imageworks/Field3D/wiki/Field3D-Home"
distfiles="https://github.com/imageworks/Field3D/archive/refs/tags/v${version}.tar.gz"
checksum=b6168bc27abe0f5e9b8d01af7794b3268ae301ac72b753712df93125d51a0fd4
+# uses hdf5 old api
+CXXFLAGS+=" -DH5_USE_110_API=1"
+
post_install() {
vlicense COPYING
}
From 1f4f9ab3738b82f76bbb893c660a82eea9db3682 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:13:01 -0300
Subject: [PATCH 03/12] flann: rebuild for hdf5
---
srcpkgs/flann/template | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/flann/template b/srcpkgs/flann/template
index af43cccd780825..9e4f38f91e2bad 100644
--- a/srcpkgs/flann/template
+++ b/srcpkgs/flann/template
@@ -1,15 +1,16 @@
# Template file for 'flann'
pkgname=flann
version=1.9.1
-revision=4
+revision=5
build_style=cmake
makedepends="gtest-devel hdf5-devel"
short_desc="Fast library for approximate nearest neighbors"
maintainer="Florian Eich <flrn@nrmncr.net>"
-license="BSD"
-homepage="http://www.cs.ubc.ca/research/${pkgname}/"
-distfiles="https://github.com/mariusmuja/${pkgname}/archive/${version}.tar.gz>${pkgname}-${version}.tar.gz"
+license="BSD-3-Clause"
+homepage="http://www.cs.ubc.ca/research/flann/"
+distfiles="https://github.com/flann-lib/flann/archive/${version}.tar.gz"
checksum=b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3
+make_check=no # broken
post_install() {
vlicense COPYING
From cc6c543196a38d064ce627082f8bd2053ce05940 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Tue, 11 Feb 2025 21:29:29 -0300
Subject: [PATCH 04/12] med: rebuild for hdf5
---
srcpkgs/med/patches/hdf5-1.14.patch | 99 ++++++++++++++++++++++++++
srcpkgs/med/patches/hdf5-version.patch | 17 +++++
srcpkgs/med/template | 3 +-
3 files changed, 118 insertions(+), 1 deletion(-)
create mode 100644 srcpkgs/med/patches/hdf5-1.14.patch
create mode 100644 srcpkgs/med/patches/hdf5-version.patch
diff --git a/srcpkgs/med/patches/hdf5-1.14.patch b/srcpkgs/med/patches/hdf5-1.14.patch
new file mode 100644
index 00000000000000..4d72add6b9fce9
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-1.14.patch
@@ -0,0 +1,99 @@
+https://salsa.debian.org/science-team/med-fichier/-/blob/master/debian/patches/hdf5-1.14.patch
+
+Index: med-fichier/config/med_check_hdf5.m4
+===================================================================
+--- med-fichier.orig/config/med_check_hdf5.m4
++++ med-fichier/config/med_check_hdf5.m4
+@@ -134,12 +134,6 @@ AC_REQUIRE([AC_PROG_GREP])
+ H5_VER_MINOR=` grep '#define *H5_VERS_MINOR' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_MINOR[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ H5_VER_RELEASE=`grep '#define *H5_VERS_RELEASE' $HDF5_ABS_PATH | sed 's/^.*H5_VERS_RELEASE[ \t]*\([0-9]*\)[ \t]*.*$/\1/g' `
+ HDF5_VERSION=` expr 10000 \* ${H5_VER_MAJOR} + 100 \* ${H5_VER_MINOR} + ${H5_VER_RELEASE} `
+- test "0${HDF5_VERSION}" -gt "11100" || test "0${HDF5_VERSION}" -lt "11002" && AC_MSG_ERROR([
+-This HDF5 version ${H5_VER_MAJOR}.${H5_VER_MINOR}.${H5_VER_RELEASE} must not be used with med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE}.
+-The HDF5 library version used by med-fichier${MED_NUM_MAJEUR}.y.z MUST NOT be > 1.10 and have to be at least HDF${HDF_VERSION_REF}.
+-DO NOT TRY TO COMPILE med-fichier${MED_NUM_MAJEUR}.${MED_NUM_MINEUR}.${MED_NUM_RELEASE} version with an HDF5 library which would generate an hdf5 file not compliant with HDF5-${HDF_VERSION_MAJOR_REF}.${HDF_VERSION_MINOR_REF}.z library.
+-This would BREAK med-fichier compatibility between files with the same revision number !
+- ])
+ else
+ ## In case user explicitly ask to not use hdf5 !
+ AC_MSG_WARN([Can't compile MED without hdf5])
+Index: med-fichier/src/ci/MEDfileCompatibility.c
+===================================================================
+--- med-fichier.orig/src/ci/MEDfileCompatibility.c
++++ med-fichier/src/ci/MEDfileCompatibility.c
+@@ -15,7 +15,6 @@
+ * along with MED. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+-
+ #include <med.h>
+ #include <med_config.h>
+ #include <med_outils.h>
+@@ -71,7 +70,7 @@ MEDfileCompatibility(const char* const f
+ _hversionMMR=10000*_hmajeur+100*_hmineur+_hrelease;
+ /* ISCRUTE(_hversionMMR); */
+ /* ISCRUTE(HDF_VERSION_NUM_REF); */
+- if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur == HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
++ if ( (_hversionMMR >= HDF_VERSION_NUM_REF) && (_hmineur >= HDF_VERSION_MINOR_REF) ) *hdfok = MED_TRUE;
+
+ /* TODO : Vérifier si la version mineure HDF du fichier est supérieure
+ à la version mineure de la bibliothèque HDF utilisée :
+@@ -114,8 +113,8 @@ MEDfileCompatibility(const char* const f
+ #error "Don't forget to update the test version here when you change the major version of the library !"
+ #endif
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
+-#error "Cf. _MEDfileCreate ..."
++#warning "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
++#warning "Cf. _MEDfileCreate ..."
+ #endif
+
+ SORTIE:
+Index: med-fichier/src/hdfi/_MEDfileCreate.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileCreate.c
++++ med-fichier/src/hdfi/_MEDfileCreate.c
+@@ -132,7 +132,7 @@ med_idt _MEDfileCreate(const char * cons
+ {
+ case 0: _release = MED_40_LATEST_RELEASE; break;
+ #if (MED_NUM_MINEUR == 0) && (MED_NUM_RELEASE > 1)
+-#error "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
++#warning "Don't forget to change the value of MED_40_LATEST_RELEASE when you change the release of version 4.0 of the library !"
+ #endif
+ /* case 1: _release = 0; break; */
+ /* case 2: _release = 1; break; */
+@@ -160,7 +160,7 @@ med_idt _MEDfileCreate(const char * cons
+ * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18 ) ) {
+Index: med-fichier/src/hdfi/_MEDfileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDfileOpen.c
++++ med-fichier/src/hdfi/_MEDfileOpen.c
+@@ -73,7 +73,7 @@ med_idt _MEDfileOpen(const char * const
+ • The creation order tracking property, H5P_CRT_ORDER_TRACKED, has been set in the group creation property list (see H5Pset_link_creation_order).
+ */
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ /* L'avantage de bloquer le modèle interne HDF5
+ est que l'on peut modifier des fichiers med de différentes versions majeures de fichiers.
+Index: med-fichier/src/hdfi/_MEDmemFileOpen.c
+===================================================================
+--- med-fichier.orig/src/hdfi/_MEDmemFileOpen.c
++++ med-fichier/src/hdfi/_MEDmemFileOpen.c
+@@ -435,7 +435,7 @@ med_idt _MEDmemFileOpen(const char * con
+ }
+
+ #if H5_VERS_MINOR > 10
+-#error "Don't forget to change the compatibility version of the library !"
++#warning "Don't forget to change the compatibility version of the library !"
+ #endif
+ if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18) ) {
+ MED_ERR_(_fid,MED_ERR_INIT,MED_ERR_PROPERTY,MED_ERR_FILEVERSION_MSG);
diff --git a/srcpkgs/med/patches/hdf5-version.patch b/srcpkgs/med/patches/hdf5-version.patch
new file mode 100644
index 00000000000000..36db2c6689906e
--- /dev/null
+++ b/srcpkgs/med/patches/hdf5-version.patch
@@ -0,0 +1,17 @@
+Don't complain on hdf5, it works with hdf5 1.14 using `-DH5_USE_110_API=1`
+
+--- a/config/cmake_files/medMacros.cmake
++++ b/config/cmake_files/medMacros.cmake
+@@ -447,9 +447,9 @@
+ ##
+ ## Requires 1.10.x version
+ ##
+- IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
+- MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
+- ENDIF()
++ # IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
++ # MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
++ # ENDIF()
+ ##
+ ##
+
diff --git a/srcpkgs/med/template b/srcpkgs/med/template
index cc553adb493e68..85151578d68825 100644
--- a/srcpkgs/med/template
+++ b/srcpkgs/med/template
@@ -14,7 +14,8 @@ homepage="https://www.salome-platform.org"
distfiles="https://github.com/chennes/med/archive/v${version}.tar.gz"
checksum=ee8b3b6d46bfee25c1d289308b16c7f248d1339161fd5448339382125e6119ad
-nocross="hdf5 is nocross"
+# uses hdf5 old api
+CFLAGS+=" -DH5_USE_110_API=1"
post_extract() {
# The py-compile helper uses the imp module, removed in Python 3.12;
From 7f3558d5ef71398b900fedbb0e457a7276af7455 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 05/12] matio: rebuild for hdf5
---
srcpkgs/matio/template | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/srcpkgs/matio/template b/srcpkgs/matio/template
index 18188e9fb2881f..1246012f338f14 100644
--- a/srcpkgs/matio/template
+++ b/srcpkgs/matio/template
@@ -1,7 +1,7 @@
# Template file for 'matio'
pkgname=matio
version=1.5.23
-revision=1
+revision=2
build_style=gnu-configure
configure_args="--disable-static"
hostmakedepends="libtool"
From 8dfa963fbc8031bddf0c8f99c6bc6de41c698d47 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 06/12] netcdf: rebuild for hdf5
---
srcpkgs/netcdf/template | 12 ++----------
1 file changed, 2 insertions(+), 10 deletions(-)
diff --git a/srcpkgs/netcdf/template b/srcpkgs/netcdf/template
index 9c1c61a89ad718..368bb64573cde2 100644
--- a/srcpkgs/netcdf/template
+++ b/srcpkgs/netcdf/template
@@ -1,11 +1,10 @@
# Template file for 'netcdf'
pkgname=netcdf
version=4.9.2
-revision=1
+revision=2
build_style=gnu-configure
-configure_args="--enable-shared"
hostmakedepends="m4"
-makedepends="libcurl-devel libxml2-devel"
+makedepends="libcurl-devel libxml2-devel hdf5-devel"
short_desc="Machine-independent format for representing scientific data"
maintainer="Hans Grob <woufrous@gmail.com>"
license="NetCDF"
@@ -14,13 +13,6 @@ distfiles="https://github.com/Unidata/netcdf-c/archive/v${version}.tar.gz"
checksum=bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7
make_check=no # https://github.com/Unidata/netcdf-c/issues/2433
-if [ "$CROSS_BUILD" ]; then
- configure_args+=" --disable-netcdf-4"
-else
- configure_args+=" --enable-netcdf-4"
- makedepends+=" hdf5-devel"
-fi
-
post_install() {
# Remove references to hardening -specs.
sed -e "s|-specs=.*hardened-ld||g" -e "s|-specs=.*hardened-cc1||g" \
From de2fa279281dc7f799a042c9278b518c4274de5d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:03 -0300
Subject: [PATCH 07/12] libgdal: rebuild for hdf5
---
srcpkgs/libgdal/template | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/srcpkgs/libgdal/template b/srcpkgs/libgdal/template
index 9a0628e3d9b26a..e712bfcccd2b64 100644
--- a/srcpkgs/libgdal/template
+++ b/srcpkgs/libgdal/template
@@ -1,7 +1,7 @@
# Template file for 'libgdal'
pkgname=libgdal
version=3.8.4
-revision=3
+revision=4
build_style=cmake
build_helper=python3
configure_args="-DGDAL_USE_OPENCL=ON
@@ -13,7 +13,7 @@ makedepends="python3-devel freexl-devel c-blosc-devel geos-devel expat-devel
libxml2-devel liblzma-devel zlib-devel libzstd-devel libdeflate-devel
netcdf-devel OpenCL-Headers pcre2-devel proj-devel sqlite-devel
ocl-icd-devel libxerces-c-devel libspatialite-devel
- postgresql-libs-devel"
+ postgresql-libs-devel hdf5-devel"
checkdepends="python3-pytest"
short_desc="Geospatial Data Abstraction Library"
maintainer="Orphaned <orphan@voidlinux.org>"
@@ -24,13 +24,12 @@ distfiles="https://download.osgeo.org/gdal/${version}/gdal-${version}.tar.xz"
checksum=0c53ced95d29474236487202709b49015854f8e02e35e44ed0f4f4e12a7966ce
python_version=3
-if [ -z "$CROSS_BUILD" ]; then
- makedepends+=" hdf5-devel"
- case "$XBPS_TARGET_MACHINE" in
- ppc|ppc-musl) ;;
- *) makedepends+=" armadillo-devel";;
- esac
-fi
+CXXFLAGS=-I$XBPS_CROSS_BASE/usr/include/python$py3_ver
+
+case "$XBPS_TARGET_MACHINE" in
+ ppc|ppc-musl) ;;
+ *) makedepends+=" armadillo-devel";;
+esac
# "error: static assertion failed: OFF_T should be 64 bits !"
if [ "$XBPS_TARGET_WORDSIZE" = "64" ]; then
From 00c191ddb712e55633aa7a1c0f4a635102704bec Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:05 -0300
Subject: [PATCH 08/12] python3-h5py: rebuild for hdf5
---
srcpkgs/python3-h5py/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/python3-h5py/template b/srcpkgs/python3-h5py/template
index c95ea6d7bee775..1928815fe79f9c 100644
--- a/srcpkgs/python3-h5py/template
+++ b/srcpkgs/python3-h5py/template
@@ -1,10 +1,10 @@
# Template file for 'python3-h5py'
pkgname=python3-h5py
version=3.13.0
-revision=1
+revision=2
build_style=python3-module
build_helper="numpy"
-hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig"
+hostmakedepends="python3-setuptools python3-Cython python3-pkgconfig hdf5-devel"
makedepends="python3-devel hdf5-devel"
depends="python3-numpy"
short_desc="HDF5 for Python"
@@ -16,6 +16,14 @@ checksum=1870e46518720023da85d0895a1960ff2ce398c5671eac3b1a41ec696b7105c3
# Tests require unpackaged pytest-mpi
make_check=no
+post_patch() {
+ if [ -n "$CROSS_BUILD" ] && [ "$XBPS_TARGET_WORDSIZE" = "32" ]; then
+ # numpy.complex256 is N/A on 32 bit; it is misdetected if host is 64 bit
+ # we need `DEF COMPLEX256_SUPPORT = False`, this seems the easiest way
+ vsed -e 's/{complex256_support}/False/' -i setup_build.py
+ fi
+}
+
pre_build() {
# Build in parallel
make_build_args+=" ${makejobs}"
From d7f42a1894538c2e4f010403e2c3d6cf2a04ff61 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 09/12] qgis: rebuild for hdf5
---
srcpkgs/qgis/template | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/srcpkgs/qgis/template b/srcpkgs/qgis/template
index d8992f76e4f635..bb7fdf9f724262 100644
--- a/srcpkgs/qgis/template
+++ b/srcpkgs/qgis/template
@@ -1,7 +1,7 @@
# Template file for 'qgis'
pkgname=qgis
version=3.40.2
-revision=1
+revision=2
build_style=cmake
configure_args="-DENABLE_TESTS=OFF -DWITH_3D=True -DWITH_PDAL=True
-DGRASS_PREFIX8=${XBPS_CROSS_BASE}/usr/lib/grass"
@@ -30,6 +30,7 @@ license="GPL-2.0-only"
homepage="https://qgis.org"
distfiles="https://github.com/qgis/QGIS/archive/final-${version//./_}.tar.gz"
checksum=83d47feceb2e3f9946e5738b6d4bd8092bc97b4836226c45883f4e5afdc50594
+nocross="due to grass"
post_install() {
mv ${DESTDIR}/usr/share/qgis/python ${DESTDIR}/usr/lib/qgis/
From 4cb37a994a94ed9e3b1dc94a4e42e5e7d5e77184 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 10/12] slurm-wlm: rebuild for hdf5
---
srcpkgs/slurm-wlm/template | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/srcpkgs/slurm-wlm/template b/srcpkgs/slurm-wlm/template
index 4405ed46fc1b1c..4029ff8f586382 100644
--- a/srcpkgs/slurm-wlm/template
+++ b/srcpkgs/slurm-wlm/template
@@ -1,15 +1,15 @@
# Template file for 'slurm-wlm'
pkgname=slurm-wlm
version=19.05.5.1
-revision=4
+revision=5
_distver="${version//./-}"
build_style=gnu-configure
configure_args="--disable-static"
-hostmakedepends="perl cgit pkg-config"
+hostmakedepends="perl python cgit pkg-config"
# XXX: ofed, DataWarp, netloc, blcr
makedepends="munge-devel lua53-devel pam-devel openssl-devel gtk+-devel
ncurses-devel readline-devel libmariadbclient-devel json-c-devel libhwloc-devel
- freeipmi-devel"
+ freeipmi-devel hdf5-devel libnuma-devel"
short_desc="Workload manager for Linux clusters of all sizes"
maintainer="Toyam Cox <Vaelatern@voidlinux.org>"
license="GPL-2.0-or-later"
@@ -31,7 +31,7 @@ fi
if [ -z "${CROSS_BUILD}" ]; then
# The below at time of writing can not be cross compiled
- makedepends+=" rrdtool-devel hdf5-devel libnuma-devel"
+ makedepends+=" rrdtool-devel"
fi
post_install() {
From e3f89d87962ada608227e0045b0dc1e3597910f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:06 -0300
Subject: [PATCH 11/12] vtk: rebuild for hdf5
---
srcpkgs/vtk/template | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/srcpkgs/vtk/template b/srcpkgs/vtk/template
index 056d5ed087cf3a..6964c221b92f8f 100644
--- a/srcpkgs/vtk/template
+++ b/srcpkgs/vtk/template
@@ -1,7 +1,7 @@
# Template file for 'vtk'
pkgname=vtk
version=9.3.1
-revision=2
+revision=3
build_style=cmake
# vtk can be huge, especially with -DVTK_BUILD_ALL_MODULES=ON"
# Build only the core modules plus python bindings for now
@@ -19,7 +19,7 @@ configure_args="-DBUILD_SHARED_LIBS=ON -DVTK_FORBID_DOWNLOADS=ON
# vtk forks libharu, bumps to v2.4.0, and requires libharu>=2.4.0
makedepends="zlib-devel freetype-devel liblz4-devel expat-devel MesaLib-devel
libXt-devel libjpeg-turbo-devel tiff-devel hdf5-devel netcdf-devel
- libxml2-devel jsoncpp-devel openmpi-devel libogg-devel libtheora-devel
+ libxml2-devel jsoncpp-devel libogg-devel libtheora-devel
eigen double-conversion-devel glew-devel pugixml-devel sqlite-devel
gl2ps-devel proj-devel python3-devel json-c++ fmt-devel"
short_desc="System for 3D computer graphics, image processing, and visualization"
@@ -28,6 +28,14 @@ license="BSD-3-Clause"
homepage="https://www.vtk.org"
distfiles="https://www.vtk.org/files/release/${version:0:3}/VTK-${version}.tar.gz"
checksum=8354ec084ea0d2dc3d23dbe4243823c4bfc270382d0ce8d658939fd50061cab8
+nocross="It seems to need vtk compile tools for the host"
+
+case "$XBPS_TARGET_MACHINE" in
+ # List of supported architectures copied from openmpi.
+ x86_64*|aarch64*|ppc64*|riscv64*)
+ makedepends+=" openmpi-devel"
+ ;;
+esac
if [ "$XBPS_TARGET_LIBC" = "musl" ]; then
makedepends+=" libexecinfo-devel"
From 81755cea7c4f35c799021c723d920e064eb8136a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Thu, 15 Aug 2024 23:08:04 -0300
Subject: [PATCH 12/12] octave: update to 9.4.0.
---
srcpkgs/octave/template | 11 +++--------
1 file changed, 3 insertions(+), 8 deletions(-)
diff --git a/srcpkgs/octave/template b/srcpkgs/octave/template
index 12c9eb50fc4fe9..2ccd93afee955d 100644
--- a/srcpkgs/octave/template
+++ b/srcpkgs/octave/template
@@ -1,6 +1,6 @@
# Template file for 'octave'
pkgname=octave
-version=9.3.0
+version=9.4.0
revision=1
build_style=gnu-configure
build_helper=qmake6
@@ -8,7 +8,7 @@ configure_args="--disable-docs"
hostmakedepends="perl gcc-fortran pkg-config qt6-base qt6-tools"
makedepends="pcre2-devel readline-devel libSM-devel libltdl-devel lcms2-devel
glpk-devel SuiteSparse-devel rapidjson arpack-ng-devel libsndfile-devel
- portaudio-devel libcurl-devel fftw-devel libgraphicsmagick-devel
+ portaudio-devel libcurl-devel fftw-devel hdf5-devel libgraphicsmagick-devel
qt6-base-devel qt6-tools-devel qt6-qt5compat-devel qt6-plugin-sqlite
qscintilla-qt6-devel glu-devel fltk-devel fontconfig-devel freetype-devel
gl2ps-devel libgomp-devel libqhull-devel zlib-devel"
@@ -20,7 +20,7 @@ license="GPL-3.0-or-later"
homepage="https://octave.org/"
changelog="http://hg.savannah.gnu.org/hgweb/octave/raw-file/default/etc/NEWS.${version%%.*}.md"
distfiles="${GNU_SITE}/octave/octave-${version}.tar.gz"
-checksum=809fa39a7acc84815bf4dc4d2d7e6b228ce75a07f3b2413f3313aa8e0aaa3287
+checksum=da9481205bfa717660b7d4a16732d8b2d58aadceab4993d41242a8e2848ea6c1
# Use OpenBLAS on platforms where it is available and fallback to regular BLAS
# on all others.
@@ -35,11 +35,6 @@ case "$XBPS_TARGET_MACHINE" in
;;
esac
-if [ -z "$CROSS_BUILD" ]; then
- # hdf5 is nocross
- makedepends+=" hdf5-devel"
-fi
-
if [ -n "$CROSS_BUILD" ];then
# cross build cannot determine integer size for BLAS
# our BLAS (lapack and openblas) are built with 32 bit ints
^ permalink raw reply [flat|nested] 19+ messages in thread
* Re: [PR PATCH] [Merged]: hdf5: update to 1.14.4.6, fix cross.
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
` (16 preceding siblings ...)
2025-03-07 19:51 ` tornaria
@ 2025-03-08 13:47 ` ahesford
17 siblings, 0 replies; 19+ messages in thread
From: ahesford @ 2025-03-08 13:47 UTC (permalink / raw)
To: ml
[-- Attachment #1: Type: text/plain, Size: 1638 bytes --]
There's a merged pull request on the void-packages repository
hdf5: update to 1.14.4.6, fix cross.
https://github.com/void-linux/void-packages/pull/51891
Description:
- **hdf5: update to 1.14.4.3, fix cross.**
- **Field3D: rebuild for hdf5**
- **flann: rebuild for hdf5**
- **med: rebuild for hdf5**
- **matio: rebuild for hdf5**
- **netcdf: rebuild for hdf5**
- **libgdal: rebuild for hdf5**
- **python3-h5py: rebuild for hdf5**
- **qgis: rebuild for hdf5**
- **slurm-wlm: rebuild for hdf5**
- **vtk: rebuild for hdf5**
- **octave: update to 9.4.0.**
~~Not rebuilt: **med** (claims to work only with hdf5 1.10, @Piraty)~~
Note: **python3-tables** is not rebuilt since it is removed.
<!-- Uncomment relevant sections and delete options which are not applicable -->
#### Testing the changes
- I tested the changes in this PR: **briefly**
<!--
#### New package
- This new package conforms to the [package requirements](https://github.com/void-linux/void-packages/blob/master/CONTRIBUTING.md#package-requirements): **YES**|**NO**
-->
<!-- Note: If the build is likely to take more than 2 hours, please add ci skip tag as described in
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and test at least one native build and, if supported, at least one cross build.
Ignore this section if this PR is not skipping CI.
-->
<!--
#### Local build testing
- I built this PR locally for my native architecture, (ARCH-LIBC)
- I built this PR locally for these architectures (if supported. mark crossbuilds):
- aarch64-musl
- armv7l
- armv6l-musl
-->
^ permalink raw reply [flat|nested] 19+ messages in thread
end of thread, other threads:[~2025-03-08 13:47 UTC | newest]
Thread overview: 19+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2024-08-17 22:58 [PR PATCH] hdf5: update to 1.14.4.3, fix cross tornaria
2024-08-18 2:45 ` [PR PATCH] [Updated] " tornaria
2024-08-18 16:19 ` tornaria
2024-08-18 20:39 ` [PR PATCH] [Updated] [WIP] " tornaria
2024-08-18 22:12 ` tornaria
2024-10-01 0:43 ` Calandracas606
2024-12-30 2:01 ` github-actions
2025-01-13 2:02 ` [PR PATCH] [Closed]: " github-actions
2025-02-11 13:46 ` classabbyamp
2025-02-12 0:40 ` [PR PATCH] [Updated] " tornaria
2025-02-12 3:02 ` tornaria
2025-02-12 15:36 ` hdf5: update to 1.14.4.6, " tornaria
2025-02-26 14:22 ` [PR PATCH] [Updated] " tornaria
2025-02-26 20:59 ` tornaria
2025-03-07 1:48 ` tornaria
2025-03-07 10:55 ` ahesford
2025-03-07 15:01 ` [PR PATCH] [Updated] " tornaria
2025-03-07 19:51 ` tornaria
2025-03-08 13:47 ` [PR PATCH] [Merged]: " ahesford
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