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-rw-r--r--sci-chemistry/erkale/metadata.xml3
-rw-r--r--sci-chemistry/relion/Manifest2
-rw-r--r--sci-chemistry/relion/files/relion-4.0.0-build.patch39
-rw-r--r--sci-chemistry/relion/metadata.xml3
-rw-r--r--sci-chemistry/relion/relion-4.0.0.ebuild (renamed from sci-chemistry/relion/relion-3.1.1.ebuild)9
5 files changed, 52 insertions, 4 deletions
diff --git a/sci-chemistry/erkale/metadata.xml b/sci-chemistry/erkale/metadata.xml
index eea62e858..996e48735 100644
--- a/sci-chemistry/erkale/metadata.xml
+++ b/sci-chemistry/erkale/metadata.xml
@@ -18,4 +18,7 @@ ground-state electron momentum densities and Compton profiles, and core
(x-ray absorption and x-ray Raman scattering) and valence electron
excitation spectra of atoms and molecules.
</longdescription>
+ <upstream>
+ <remote-id type="github">susilehtola/erkale</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/relion/Manifest b/sci-chemistry/relion/Manifest
index 6aa383614..058ff2285 100644
--- a/sci-chemistry/relion/Manifest
+++ b/sci-chemistry/relion/Manifest
@@ -1 +1 @@
-DIST relion-3.1.1.tar.gz 2340685 BLAKE2B 0e98db3af7ceb312111260d8af51225d9a6b82314f1f066fe52464b533e59f44f5487ba66110708d661506074be4d52eeb7e04d88344a939bbd33139a33f6dec SHA512 fddf6f8a3d63e4f73aa1f529e4fa8fa7da98d9226b6539530c83496b94793ceef27d013a2d902a794993ab994f8d6467569ea4b681b4dd948654acf482529b22
+DIST relion-4.0.0.tar.gz 3342593 BLAKE2B d2293531cdf3c5779a8f6beb5bc753931388f1c577faa89a927c6ccd72436db0d9a84fbe08b836601b466bc23e9df6500f9e87da1630adecd2b0cf0e245d63e6 SHA512 1e873868bc54a13a7cca74c4a623f5f2aeeec7bd2df04f74d0421127a9c9a3b40a56ebc5b04a9f4138cca1208417b05a30c38ae78106d53b92deeadbeeaf4209
diff --git a/sci-chemistry/relion/files/relion-4.0.0-build.patch b/sci-chemistry/relion/files/relion-4.0.0-build.patch
new file mode 100644
index 000000000..d7cb7bf2e
--- /dev/null
+++ b/sci-chemistry/relion/files/relion-4.0.0-build.patch
@@ -0,0 +1,39 @@
+From 138b9c71b41a3c8782c991053a28bfe074bffdd9 Mon Sep 17 00:00:00 2001
+From: Takanori Nakane <nakane.t@gmail.com>
+Date: Fri, 28 Oct 2022 19:51:29 +0900
+Subject: [PATCH] Repaired the build failure reported in #826 (by
+ @prehensilecode and @acaprez)
+
+---
+ src/apps/CMakeLists.txt | 16 ++++++++--------
+ 1 file changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/src/apps/CMakeLists.txt b/src/apps/CMakeLists.txt
+index 9870b735..30985aa7 100644
+--- a/src/apps/CMakeLists.txt
++++ b/src/apps/CMakeLists.txt
+@@ -273,16 +273,16 @@ if (CUDA_FOUND)
+
+
+
+- file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu" "${CMAKE_SOURCE_DIR}/src/jaz/cuda/kernels/*.cu" )
++ file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu")
+ cuda_add_library(relion_jaz_gpu_util ${REL_JAZ_CUDA_SRC})
+
+- #list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}")
+- #if(BUILD_SHARED_LIBS)
+- # install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib)
+- #else()
+- # target_link_libraries(relion_jaz_gpu_util relion_lib)
+- # target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
+- #endif()
++ list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}")
++ if(BUILD_SHARED_LIBS)
++ install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib)
++ else()
++ target_link_libraries(relion_jaz_gpu_util relion_lib)
++ target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
++ endif()
+
+ target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES})
+ target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES} ${CUDA_curand_LIBRARY})
diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml
index cdabe7f2c..33e6e7e5d 100644
--- a/sci-chemistry/relion/metadata.xml
+++ b/sci-chemistry/relion/metadata.xml
@@ -12,4 +12,7 @@
<use>
<flag name="gui">Enable relion gui</flag>
</use>
+ <upstream>
+ <remote-id type="github">3dem/relion</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/sci-chemistry/relion/relion-3.1.1.ebuild b/sci-chemistry/relion/relion-4.0.0.ebuild
index 39e4ab229..a40375f64 100644
--- a/sci-chemistry/relion/relion-3.1.1.ebuild
+++ b/sci-chemistry/relion/relion-4.0.0.ebuild
@@ -1,7 +1,7 @@
# Copyright 2019-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
inherit cmake
@@ -12,10 +12,11 @@ SRC_URI="https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="+gui"
+IUSE="+gui cuda"
DEPEND="
gui? ( x11-libs/fltk )
+ cuda? ( dev-util/nvidia-cuda-toolkit )
dev-cpp/tbb
sci-libs/fftw:3.0
media-libs/tiff
@@ -27,6 +28,8 @@ RDEPEND="
"
BDEPEND="${DEPEND}"
+PATCHES=( "${FILESDIR}/${PN}-4.0.0-build.patch" )
+
src_configure() {
CMAKE_BUILD_TYPE=Release
mycmakeargs=(
@@ -35,7 +38,7 @@ src_configure() {
-DFORCE_OWN_FFTW=OFF
-DFORCE_OWN_FLTK=OFF
-DFORCE_OWN_TBB=OFF
- -DCUDA=OFF
+ -DCUDA=$(usex cuda)
-DGUI=$(usex gui)
)
cmake_src_configure