* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2019-11-25 18:30 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2019-11-25 18:30 UTC (permalink / raw
To: gentoo-commits
commit: b3db3a9c0d4b6e6a7c24003a12eef93e4a79c73d
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Nov 25 18:30:38 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Nov 25 18:30:38 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b3db3a9c
sci-biology/afni: version bump 19.3.12 (non-masked version)
Package-Manager: Portage-2.3.79, Repoman-2.3.18
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-19.3.12.ebuild | 72 ++++++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/sci-biology/afni/afni-19.3.12.ebuild b/sci-biology/afni/afni-19.3.12.ebuild
new file mode 100644
index 000000000..c60a87138
--- /dev/null
+++ b/sci-biology/afni/afni-19.3.12.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils multilib pax-utils toolchain-funcs
+
+DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
+HOMEPAGE="http://afni.nimh.nih.gov/"
+SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sys-devel/llvm:*
+ virtual/jpeg:0
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXpm
+ x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${RDEPEND}
+ app-shells/tcsh"
+
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
+BUILD="linux_fedora_19_64"
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+src_prepare() {
+ find -type f -exec sed -i -e "s/-lXp //g" {} +
+ cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
+ # Unbundle imcat
+ sed -e "s/ imcat / /g" \
+ -i Makefile.INCLUDE || die "Could not edit includes files."
+ sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
+ -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
+ -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
+ -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
+ -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
+ -i Makefile || die "Could not edit Makefile"
+ # they provide somewhat problematic makefiles :(
+ sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
+ -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
+ # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ eapply_user
+}
+
+src_compile() {
+ emake -j1 all plugins suma_exec
+}
+
+src_install() {
+ emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
+ emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
+ for CONFLICT in ${BIN_CONFLICTS[@]}; do
+ rm "${ED}/usr/bin/${CONFLICT}"
+ done
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2024-05-30 21:55 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2024-05-30 21:55 UTC (permalink / raw
To: gentoo-commits
commit: be6977739d20a779f291c66eefb9cc896ff2e4e0
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu May 30 21:55:24 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu May 30 21:55:24 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=be697773
sci-biology/afni: drop 24.0.04-r1, 24.0.08-r1, 24.0.08-r2
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-24.0.04-r1.ebuild | 110 ----------------------------
sci-biology/afni/afni-24.0.08-r1.ebuild | 114 -----------------------------
sci-biology/afni/afni-24.0.08-r2.ebuild | 124 --------------------------------
3 files changed, 348 deletions(-)
diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild
deleted file mode 100644
index c5adfb6d8..000000000
--- a/sci-biology/afni/afni-24.0.04-r1.ebuild
+++ /dev/null
@@ -1,110 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..13} )
-
-DISTUTILS_USE_PEP517=setuptools
-inherit cmake distutils-r1 toolchain-funcs
-
-GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
-NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
-GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
-
-DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
-HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
-SRC_URI="
- https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
- https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
- https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
- "
-
-S="${WORKDIR}/afni-AFNI_${PV}"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test whirlgif"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-libs/glib:2
- dev-libs/libf2c
- dev-libs/expat
- dev-build/ninja
- media-libs/freeglut
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sci-libs/gts
- sys-devel/llvm:*
- sys-libs/libomp
- virtual/jpeg-compat:62
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXmu
- x11-libs/libXpm
- x11-libs/libXt
- x11-libs/motif[-static-libs]
- "
-DEPEND="
- ${RDEPEND}
- app-shells/tcsh
- "
-
-src_prepare() {
- tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
- tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
- cmake_src_prepare
- default
- }
-
-src_configure() {
- if use !whirlgif; then
- eapply "${FILESDIR}/${P}-whirlgif.patch"
- fi
- export CFLAGS="-pthread ${CFLAGS}"
- export GIT_REPO_VERSION=3.0.1.1
- local mycmakeargs=(
- -DLIBDIR=/usr/$(get_libdir)
- -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
- -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
- -DCOMP_COREBINARIES=ON
- -DUSE_SYSTEM_NIFTI=OFF
- -DUSE_SYSTEM_GIFTI=OFF
- -DUSE_SYSTEM_XMHTML=OFF
- -DUSE_SYSTEM_GTS=ON
- -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
- -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
- -DCOMP_GUI=ON
- -DCOMP_PLUGINS=ON
- -DUSE_OMP=ON
- -DCOMP_PYTHON=OFF
- -DUSE_SYSTEM_F2C=ON
- )
- tc-export CC
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- pushd src/python_scripts
- distutils-r1_src_compile
- popd
-}
-
-src_install() {
- cmake_src_install
- pushd src/python_scripts
- distutils-r1_src_install
- popd
- cd "${D}"
- rm usr/bin/mpeg_encode
-}
diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild
deleted file mode 100644
index 21ecf81a1..000000000
--- a/sci-biology/afni/afni-24.0.08-r1.ebuild
+++ /dev/null
@@ -1,114 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..13} )
-
-DISTUTILS_USE_PEP517=setuptools
-inherit cmake distutils-r1 toolchain-funcs
-
-GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
-NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
-GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
-
-DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
-HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
-SRC_URI="
- https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
- https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
- https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
- "
-
-S="${WORKDIR}/afni-AFNI_${PV}"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test whirlgif"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-libs/glib:2
- dev-libs/libf2c
- dev-libs/expat
- dev-build/ninja
- media-libs/freeglut
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sci-libs/gts
- sys-devel/llvm:*
- sys-libs/libomp
- virtual/jpeg-compat:62
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXmu
- x11-libs/libXpm
- x11-libs/libXt
- x11-libs/motif[-static-libs]
- "
-DEPEND="
- ${RDEPEND}
- app-shells/tcsh
- "
-# Prospectively:
-#Update jpeg-compat to virtual/jpeg:0
-# look for xmhtlm
-
- #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
-src_prepare() {
- tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
- tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
- cmake_src_prepare
- default
- }
-
-src_configure() {
- if use !whirlgif; then
- eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
- fi
- export CFLAGS="-pthread ${CFLAGS}"
- export GIT_REPO_VERSION=3.0.1.1
- local mycmakeargs=(
- -DLIBDIR=/usr/$(get_libdir)
- -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
- -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
- -DCOMP_COREBINARIES=ON
- -DUSE_SYSTEM_NIFTI=OFF
- -DUSE_SYSTEM_GIFTI=OFF
- -DUSE_SYSTEM_XMHTML=OFF
- -DUSE_SYSTEM_GTS=ON
- -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
- -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
- -DCOMP_GUI=ON
- -DCOMP_PLUGINS=ON
- -DUSE_OMP=ON
- -DCOMP_PYTHON=OFF
- -DUSE_SYSTEM_F2C=ON
- )
- tc-export CC
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- pushd src/python_scripts
- distutils-r1_src_compile
- popd
-}
-
-src_install() {
- cmake_src_install
- pushd src/python_scripts
- distutils-r1_src_install
- popd
- cd "${D}"
- rm usr/bin/mpeg_encode
-}
diff --git a/sci-biology/afni/afni-24.0.08-r2.ebuild b/sci-biology/afni/afni-24.0.08-r2.ebuild
deleted file mode 100644
index 270100c0b..000000000
--- a/sci-biology/afni/afni-24.0.08-r2.ebuild
+++ /dev/null
@@ -1,124 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..13} )
-
-DISTUTILS_USE_PEP517=setuptools
-inherit cmake distutils-r1 toolchain-funcs
-
-GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
-NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
-GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
-
-DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
-HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
-SRC_URI="
- https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
- https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
- https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
- "
-
-S="${WORKDIR}/afni-AFNI_${PV}"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test whirlgif"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-build/ninja
- dev-libs/expat
- dev-libs/glib:2
- dev-libs/libf2c
- media-libs/freeglut
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-biology/afni-datasets
- sci-libs/gsl
- sci-libs/gts
- sys-devel/llvm:*
- sys-libs/libomp
- virtual/jpeg-compat:62
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXmu
- x11-libs/libXpm
- x11-libs/libXt
- x11-libs/motif[-static-libs]
- "
-DEPEND="
- ${RDEPEND}
- app-shells/tcsh
- "
-# Prospectively:
-#Update jpeg-compat to virtual/jpeg:0
-# look for xmhtlm
-
- #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
-src_prepare() {
- tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
- tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
- cmake_src_prepare
- default
- }
-
-src_configure() {
- if use !whirlgif; then
- eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
- fi
- export CFLAGS="-pthread ${CFLAGS}"
- export GIT_REPO_VERSION=3.0.1.1
- local mycmakeargs=(
- -DLIBDIR=/usr/$(get_libdir)
- -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
- -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
- -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
- -DCOMP_COREBINARIES=ON
- -DUSE_SYSTEM_NIFTI=OFF
- -DUSE_SYSTEM_GIFTI=OFF
- -DUSE_SYSTEM_XMHTML=OFF
- -DUSE_SYSTEM_GTS=ON
- -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
- -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
- -DCOMP_GUI=ON
- -DCOMP_PLUGINS=ON
- -DUSE_OMP=ON
- -DCOMP_PYTHON=OFF
- -DUSE_SYSTEM_F2C=ON
- )
- tc-export CC
- cmake_src_configure
-}
-
-src_compile() {
- cmake_src_compile
- pushd src/python_scripts
- distutils-r1_src_compile
- popd
-}
-
-src_install() {
- cmake_src_install
- pushd src/python_scripts
- distutils-r1_src_install
- popd
- cd "${D}"
- rm usr/bin/mpeg_encode
- doenvd "${FILESDIR}/97afni"
-}
-
-pkg_postinst() {
- echo
- einfo "Please run the following commands if you"
- einfo "intend to use afni binaries from an existing shell:"
- einfo "source /etc/profile"
- echo
-}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2024-05-29 8:33 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2024-05-29 8:33 UTC (permalink / raw
To: gentoo-commits
commit: 6d9b772f10ed51682604e5c1cb6f9c278a5c6c72
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed May 29 08:31:29 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed May 29 08:31:29 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d9b772f
sci-biology/afni: correct version annotation
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-24.0.08-r3.ebuild | 125 ++++++++++++++++++++++++++++++++
1 file changed, 125 insertions(+)
diff --git a/sci-biology/afni/afni-24.0.08-r3.ebuild b/sci-biology/afni/afni-24.0.08-r3.ebuild
new file mode 100644
index 000000000..12d6c8f87
--- /dev/null
+++ b/sci-biology/afni/afni-24.0.08-r3.ebuild
@@ -0,0 +1,125 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+
+DISTUTILS_USE_PEP517=setuptools
+inherit cmake distutils-r1 toolchain-funcs
+
+GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
+NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
+GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
+
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
+SRC_URI="
+ https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
+ https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
+ https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
+ "
+
+S="${WORKDIR}/afni-AFNI_${PV}"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test whirlgif"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-build/ninja
+ dev-libs/expat
+ dev-libs/glib:2
+ dev-libs/libf2c
+ media-libs/freeglut
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-biology/afni-datasets
+ sci-libs/gsl
+ sci-libs/gts
+ sys-devel/llvm:*
+ sys-libs/libomp
+ virtual/jpeg-compat:62
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXmu
+ x11-libs/libXpm
+ x11-libs/libXt
+ x11-libs/motif[-static-libs]
+ "
+DEPEND="
+ ${RDEPEND}
+ app-shells/tcsh
+ "
+# Prospectively:
+#Update jpeg-compat to virtual/jpeg:0
+# look for xmhtlm
+
+ #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
+src_prepare() {
+ tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
+ tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
+ cmake_src_prepare
+ default
+ }
+
+src_configure() {
+ if use !whirlgif; then
+ eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch"
+ fi
+ # Fix AFNI version, no better way seemed to work
+ sed -i -e "s/GIT_REPO_VERSION \"99\.99\.99\"/GIT_REPO_VERSION ${PV}/g" cmake/get_git_repo_version.cmake
+ export CFLAGS="-pthread ${CFLAGS}"
+ local mycmakeargs=(
+ -DLIBDIR=/usr/$(get_libdir)
+ -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir)
+ -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir)
+ -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir)
+ -DCOMP_COREBINARIES=ON
+ -DUSE_SYSTEM_NIFTI=OFF
+ -DUSE_SYSTEM_GIFTI=OFF
+ -DUSE_SYSTEM_XMHTML=OFF
+ -DUSE_SYSTEM_GTS=ON
+ -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}"
+ -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}"
+ -DCOMP_GUI=ON
+ -DCOMP_PLUGINS=ON
+ -DUSE_OMP=ON
+ -DCOMP_PYTHON=OFF
+ -DUSE_SYSTEM_F2C=ON
+ )
+ tc-export CC
+ cmake_src_configure
+}
+
+src_compile() {
+ cmake_src_compile
+ pushd src/python_scripts
+ distutils-r1_src_compile
+ popd
+}
+
+src_install() {
+ cmake_src_install
+ pushd src/python_scripts
+ distutils-r1_src_install
+ popd
+ cd "${D}"
+ rm usr/bin/mpeg_encode
+ doenvd "${FILESDIR}/97afni"
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use afni binaries from an existing shell:"
+ einfo "source /etc/profile"
+ echo
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2024-05-24 13:52 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2024-05-24 13:52 UTC (permalink / raw
To: gentoo-commits
commit: b5ce4a1154c05787fe20c3074b2bc91f5146bacf
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri May 24 13:49:20 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri May 24 13:49:20 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b5ce4a11
sci-biology/afni: update DESCRIPTION, HOMEPAGE
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-24.0.04-r1.ebuild | 12 ++++++------
sci-biology/afni/afni-24.0.08-r1.ebuild | 12 ++++++------
2 files changed, 12 insertions(+), 12 deletions(-)
diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild
index 557fbd579..c5adfb6d8 100644
--- a/sci-biology/afni/afni-24.0.04-r1.ebuild
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
DISTUTILS_USE_PEP517=setuptools
inherit cmake distutils-r1 toolchain-funcs
@@ -12,16 +12,18 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/"
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
SRC_URI="
https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
"
-SLOT="0"
+S="${WORKDIR}/afni-AFNI_${PV}"
+
LICENSE="GPL-3+"
+SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="test whirlgif"
RESTRICT="!test? ( test )"
@@ -54,8 +56,6 @@ DEPEND="
app-shells/tcsh
"
-S="${WORKDIR}/afni-AFNI_${PV}"
-
src_prepare() {
tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die
diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild
index 20293877f..21ecf81a1 100644
--- a/sci-biology/afni/afni-24.0.08-r1.ebuild
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..12} )
+PYTHON_COMPAT=( python3_{10..13} )
DISTUTILS_USE_PEP517=setuptools
inherit cmake distutils-r1 toolchain-funcs
@@ -12,16 +12,18 @@ GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7"
NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c"
GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7"
-DESCRIPTION="Advanced Normalitazion Tools for neuroimaging"
-HOMEPAGE="http://stnava.github.io/ANTs/"
+DESCRIPTION="Analysis of Functional Neuroimages by NIMH"
+HOMEPAGE="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/"
SRC_URI="
https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz
https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz
https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz
"
-SLOT="0"
+S="${WORKDIR}/afni-AFNI_${PV}"
+
LICENSE="GPL-3+"
+SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="test whirlgif"
RESTRICT="!test? ( test )"
@@ -57,8 +59,6 @@ DEPEND="
#Update jpeg-compat to virtual/jpeg:0
# look for xmhtlm
-S="${WORKDIR}/afni-AFNI_${PV}"
-
#tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die
src_prepare() {
tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2024-03-22 21:34 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2024-03-22 21:34 UTC (permalink / raw
To: gentoo-commits
commit: bf635e42b9e981623432224920b21940f4feda56
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Mar 22 21:18:40 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Mar 22 21:18:40 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=bf635e42
sci-biology/afni: removed deprecated deps
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/{afni-24.0.04.ebuild => afni-24.0.04-r1.ebuild} | 1 -
sci-biology/afni/{afni-24.0.08.ebuild => afni-24.0.08-r1.ebuild} | 1 -
2 files changed, 2 deletions(-)
diff --git a/sci-biology/afni/afni-24.0.04.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild
similarity index 98%
rename from sci-biology/afni/afni-24.0.04.ebuild
rename to sci-biology/afni/afni-24.0.04-r1.ebuild
index c00ef846f..557fbd579 100644
--- a/sci-biology/afni/afni-24.0.04.ebuild
+++ b/sci-biology/afni/afni-24.0.04-r1.ebuild
@@ -40,7 +40,6 @@ RDEPEND="
sci-libs/gts
sys-devel/llvm:*
sys-libs/libomp
- dev-libs/libpthread-stubs
virtual/jpeg-compat:62
x11-libs/libGLw
x11-libs/libXft
diff --git a/sci-biology/afni/afni-24.0.08.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild
similarity index 99%
rename from sci-biology/afni/afni-24.0.08.ebuild
rename to sci-biology/afni/afni-24.0.08-r1.ebuild
index 75ff5b6b6..20293877f 100644
--- a/sci-biology/afni/afni-24.0.08.ebuild
+++ b/sci-biology/afni/afni-24.0.08-r1.ebuild
@@ -40,7 +40,6 @@ RDEPEND="
sci-libs/gts
sys-devel/llvm:*
sys-libs/libomp
- dev-libs/libpthread-stubs
virtual/jpeg-compat:62
x11-libs/libGLw
x11-libs/libXft
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2022-04-03 8:11 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2022-04-03 8:11 UTC (permalink / raw
To: gentoo-commits
commit: 65c6f547d13f0bf646544e6aef04a70e0d8976c3
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Apr 3 08:11:12 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Apr 3 08:11:12 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=65c6f547
sci-biology/afni: corrected patch application
ebuild still fails, though, log included in comment and reposited here:
https://ppb.chymera.eu/4223de.log
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-22.0.21.ebuild | 10 +++-------
1 file changed, 3 insertions(+), 7 deletions(-)
diff --git a/sci-biology/afni/afni-22.0.21.ebuild b/sci-biology/afni/afni-22.0.21.ebuild
index d8ad693bf..6694c9525 100644
--- a/sci-biology/afni/afni-22.0.21.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -12,8 +12,7 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
LICENSE="GPL-3+"
SLOT="0"
-# Depends on some python version withoug pulling it in
-# `thd_selenium.c:18:10: fatal error: Python.h: No such file or directory`
+# SUMA error: https://ppb.chymera.eu/4223de.log
KEYWORDS=""
RDEPEND="
@@ -38,15 +37,12 @@ DEPEND="${RDEPEND}
app-shells/tcsh
"
-PATCHES=(
- # Drop python2.7 dependency
- "${FILESDIR}/${P}-python.patch"
-)
-
BUILD="linux_fedora_19_64"
BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count)
src_prepare() {
+ # more easily applied here than via PATCHES at phase end.
+ eapply "${FILESDIR}/${P}-python.patch" || die
find -type f -exec sed -i -e "s/-lXp //g" {} + || die
cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
# Unbundle imcat
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2022-04-01 15:41 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2022-04-01 15:41 UTC (permalink / raw
To: gentoo-commits
commit: e076bdf17bc9d27acebb0294bc5fab198ffd91f5
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Apr 1 15:41:23 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Apr 1 15:41:23 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e076bdf1
sci-biology/afni: bump ebuild still fails
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-22.0.21.ebuild | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/sci-biology/afni/afni-22.0.21.ebuild b/sci-biology/afni/afni-22.0.21.ebuild
index 5a015dafc..d8ad693bf 100644
--- a/sci-biology/afni/afni-22.0.21.ebuild
+++ b/sci-biology/afni/afni-22.0.21.ebuild
@@ -12,7 +12,9 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
LICENSE="GPL-3+"
SLOT="0"
-KEYWORDS="~amd64"
+# Depends on some python version withoug pulling it in
+# `thd_selenium.c:18:10: fatal error: Python.h: No such file or directory`
+KEYWORDS=""
RDEPEND="
dev-libs/libf2c
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2022-04-01 8:22 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2022-04-01 8:22 UTC (permalink / raw
To: gentoo-commits
commit: e3ed6312407f673e0d8d544fd54d625b6492a27a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Apr 1 08:22:33 2022 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Apr 1 08:22:33 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e3ed6312
sci-biology/afni: cleaned up whitespace and unneeded code
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-20.1.16.ebuild | 8 ++++----
sci-biology/afni/afni-20.3.03.ebuild | 6 +-----
2 files changed, 5 insertions(+), 9 deletions(-)
diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
index 98fdb2397..a95a34cfb 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -46,17 +46,17 @@ src_prepare() {
# Unbundle imcat
sed -e "s/ imcat / /g" \
-i Makefile.INCLUDE || die "Could not edit includes files."
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
+ sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
-e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
+ -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
+ -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
-e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
-i Makefile || die "Could not edit Makefile"
# they provide somewhat problematic makefiles :(
sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
default
}
diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
index fab7446bf..a95a34cfb 100644
--- a/sci-biology/afni/afni-20.3.03.ebuild
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -39,10 +39,6 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
BUILD="linux_fedora_19_64"
BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-#PATCHES=(
-# "${FILESDIR}/${P}-python.patch"
-#)
-
src_prepare() {
eapply "${FILESDIR}/${P}-python.patch" || die
find -type f -exec sed -i -e "s/-lXp //g" {} +
@@ -60,7 +56,7 @@ src_prepare() {
sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
-i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
# upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i
default
}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2021-01-03 3:46 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2021-01-03 3:46 UTC (permalink / raw
To: gentoo-commits
commit: 5c191a775d0dedfe49d26f2bc38342791f8750b7
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Jan 3 03:46:05 2021 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan 3 03:46:05 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c191a77
sci-biology/afni: version bump 20.3.03
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-20.3.03.ebuild | 77 ++++++++++++++++++++++++++++++++++++
1 file changed, 77 insertions(+)
diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild
new file mode 100644
index 000000000..ed100cb3c
--- /dev/null
+++ b/sci-biology/afni/afni-20.3.03.ebuild
@@ -0,0 +1,77 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils multilib pax-utils toolchain-funcs
+
+DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
+HOMEPAGE="http://afni.nimh.nih.gov/"
+SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sys-devel/llvm:*
+ virtual/jpeg:0
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXpm
+ x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${RDEPEND}
+ app-shells/tcsh"
+
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
+BUILD="linux_fedora_19_64"
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+#PATCHES=(
+# "${FILESDIR}/${P}-python.patch"
+#)
+
+src_prepare() {
+ eapply "${FILESDIR}/${P}-python.patch" || die
+ find -type f -exec sed -i -e "s/-lXp //g" {} +
+ cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
+ # Unbundle imcat
+ sed -e "s/ imcat / /g" \
+ -i Makefile.INCLUDE || die "Could not edit includes files."
+ sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
+ -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
+ -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
+ -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
+ -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
+ -i Makefile || die "Could not edit Makefile"
+ # they provide somewhat problematic makefiles :(
+ sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
+ -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
+ # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ default
+}
+
+src_compile() {
+ emake -j1 all plugins suma_exec
+}
+
+src_install() {
+ emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
+ emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
+ for CONFLICT in ${BIN_CONFLICTS[@]}; do
+ rm "${ED}/usr/bin/${CONFLICT}"
+ done
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2021-01-03 3:46 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2021-01-03 3:46 UTC (permalink / raw
To: gentoo-commits
commit: f225be3cfea18d5fedcc3c7f77f402effa123dea
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Jan 3 03:44:38 2021 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Jan 3 03:44:38 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f225be3c
sci-biology/afni: applying patch at start of prepare phase
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-20.1.16.ebuild | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
index 09e2b7def..da68d2d6d 100644
--- a/sci-biology/afni/afni-20.1.16.ebuild
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -39,11 +39,8 @@ S="${WORKDIR}/${PN}-AFNI_${PV}/src"
BUILD="linux_fedora_19_64"
BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-PATCHES=(
- "${FILESDIR}/${P}-python.patch"
-)
-
src_prepare() {
+ eapply "${FILESDIR}/${P}-python.patch" || die
find -type f -exec sed -i -e "s/-lXp //g" {} +
cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
# Unbundle imcat
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2020-06-19 16:01 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2020-06-19 16:01 UTC (permalink / raw
To: gentoo-commits
commit: 644434c14f22d95edcf230733955076ecab0cf31
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jun 19 16:01:29 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jun 19 16:01:29 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=644434c1
sci-biology/afni: version bump 20.1.16
Package-Manager: Portage-2.3.101, Repoman-2.3.22
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-20.1.16.ebuild | 72 ++++++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild
new file mode 100644
index 000000000..4953408d6
--- /dev/null
+++ b/sci-biology/afni/afni-20.1.16.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit eutils multilib pax-utils toolchain-funcs
+
+DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
+HOMEPAGE="http://afni.nimh.nih.gov/"
+SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="dev-libs/expat
+ media-libs/glu
+ media-libs/netpbm
+ media-libs/qhull
+ media-video/mpeg-tools
+ sci-libs/gsl
+ sys-devel/llvm:*
+ virtual/jpeg:0
+ x11-libs/libGLw
+ x11-libs/libXft
+ x11-libs/libXi
+ x11-libs/libXpm
+ x11-libs/motif[-static-libs]"
+
+# x11-libs/motif[static-libs] breaks the build.
+# See upstream discussion
+# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
+
+DEPEND="${RDEPEND}
+ app-shells/tcsh"
+
+S="${WORKDIR}/${PN}-AFNI_${PV}/src"
+BUILD="linux_fedora_19_64"
+BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
+
+src_prepare() {
+ find -type f -exec sed -i -e "s/-lXp //g" {} +
+ cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
+ # Unbundle imcat
+ sed -e "s/ imcat / /g" \
+ -i Makefile.INCLUDE || die "Could not edit includes files."
+ sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
+ -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
+ -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
+ -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
+ -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
+ -i Makefile || die "Could not edit Makefile"
+ # they provide somewhat problematic makefiles :(
+ sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
+ -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
+ # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
+ find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
+ eapply_user
+}
+
+src_compile() {
+ emake -j1 all plugins suma_exec
+}
+
+src_install() {
+ emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
+ emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib
+ for CONFLICT in ${BIN_CONFLICTS[@]}; do
+ rm "${ED}/usr/bin/${CONFLICT}"
+ done
+}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2020-01-16 18:28 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2020-01-16 18:28 UTC (permalink / raw
To: gentoo-commits
commit: ab307a97b24eb48f5e7c7e7570a0486d07111148
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Jan 16 18:27:52 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Jan 16 18:27:52 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab307a97
sci-biology/afni: deprecated old hard-masked versions
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-18.1.04.ebuild | 69 ------------------------------------
sci-biology/afni/afni-19.0.21.ebuild | 69 ------------------------------------
2 files changed, 138 deletions(-)
diff --git a/sci-biology/afni/afni-18.1.04.ebuild b/sci-biology/afni/afni-18.1.04.ebuild
deleted file mode 100644
index c3f1be074..000000000
--- a/sci-biology/afni/afni-18.1.04.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils multilib pax-utils toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- virtual/jpeg:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
- eapply_user
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
diff --git a/sci-biology/afni/afni-19.0.21.ebuild b/sci-biology/afni/afni-19.0.21.ebuild
deleted file mode 100644
index c3f1be074..000000000
--- a/sci-biology/afni/afni-19.0.21.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit eutils multilib pax-utils toolchain-funcs
-
-DESCRIPTION="An open-source environment for processing and displaying functional MRI data"
-HOMEPAGE="http://afni.nimh.nih.gov/"
-SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="dev-libs/expat
- media-libs/glu
- media-libs/netpbm
- media-libs/qhull
- media-video/mpeg-tools
- sci-libs/gsl
- sys-devel/llvm:*
- virtual/jpeg:0
- x11-libs/libGLw
- x11-libs/libXft
- x11-libs/libXi
- x11-libs/libXpm
- x11-libs/motif[-static-libs]"
-
-# x11-libs/motif[static-libs] breaks the build.
-# See upstream discussion
-# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348
-
-DEPEND="${RDEPEND}
- app-shells/tcsh"
-
-S="${WORKDIR}/${PN}-AFNI_${PV}/src"
-BUILD="linux_fedora_19_64"
-BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode)
-
-src_prepare() {
- find -type f -exec sed -i -e "s/-lXp //g" {} +
- cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile"
- sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \
- -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \
- -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \
- -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \
- -i Makefile || die "Could not edit Makefile"
- # they provide somewhat problematic makefiles :(
- sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\
- -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile"
- # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac
- find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EROOT}/usr/~g;" -i
- eapply_user
-}
-
-src_compile() {
- emake -j1 all plugins suma_exec
-}
-
-src_install() {
- emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins
- emake INSTALLDIR="${ED}/usr/$(get_libdir)" -j1 install_lib
- for CONFLICT in ${BIN_CONFLICTS[@]}; do
- rm "${ED}/usr/bin/${CONFLICT}"
- done
-}
^ permalink raw reply related [flat|nested] 14+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2019-04-25 8:50 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2019-04-25 8:50 UTC (permalink / raw
To: gentoo-commits
commit: d4ca0e569b7e7f01c39bd08adb2b8c42efa96be0
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Thu Apr 25 08:48:41 2019 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Thu Apr 25 08:50:33 2019 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d4ca0e56
sci-biology/afni: dependency update
Package-Manager: Portage-2.3.63, Repoman-2.3.12
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/afni/afni-18.1.04.ebuild | 3 ++-
sci-biology/afni/afni-19.0.21.ebuild | 1 +
sci-biology/afni/afni-9999.ebuild | 3 ++-
3 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/afni/afni-18.1.04.ebuild b/sci-biology/afni/afni-18.1.04.ebuild
index ba1a0bcd9..c3f1be074 100644
--- a/sci-biology/afni/afni-18.1.04.ebuild
+++ b/sci-biology/afni/afni-18.1.04.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -15,6 +15,7 @@ KEYWORDS="~amd64 ~x86"
IUSE=""
RDEPEND="dev-libs/expat
+ media-libs/glu
media-libs/netpbm
media-libs/qhull
media-video/mpeg-tools
diff --git a/sci-biology/afni/afni-19.0.21.ebuild b/sci-biology/afni/afni-19.0.21.ebuild
index 104015772..c3f1be074 100644
--- a/sci-biology/afni/afni-19.0.21.ebuild
+++ b/sci-biology/afni/afni-19.0.21.ebuild
@@ -15,6 +15,7 @@ KEYWORDS="~amd64 ~x86"
IUSE=""
RDEPEND="dev-libs/expat
+ media-libs/glu
media-libs/netpbm
media-libs/qhull
media-video/mpeg-tools
diff --git a/sci-biology/afni/afni-9999.ebuild b/sci-biology/afni/afni-9999.ebuild
index e73bef8cc..e30be5542 100644
--- a/sci-biology/afni/afni-9999.ebuild
+++ b/sci-biology/afni/afni-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -16,6 +16,7 @@ KEYWORDS=""
IUSE=""
RDEPEND="dev-libs/expat
+ media-libs/glu
media-libs/netpbm
media-libs/qhull
media-video/mpeg-tools
^ permalink raw reply related [flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/afni/
@ 2018-06-26 1:16 Horea Christian
0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2018-06-26 1:16 UTC (permalink / raw
To: gentoo-commits
commit: 8536fe8cb8687e2b585d3f805affbf17971b9653
Author: Horea Christian <horea.christ <AT> yandex <DOT> com>
AuthorDate: Tue Jun 26 01:16:34 2018 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jun 26 01:16:34 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8536fe8c
sci-biology/afni: Added unstable x86 keyword
Package-Manager: Portage-2.3.40, Repoman-2.3.9
sci-biology/afni/afni-18.1.04.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/afni/afni-18.1.04.ebuild b/sci-biology/afni/afni-18.1.04.ebuild
index 3a646ffb7..ba1a0bcd9 100644
--- a/sci-biology/afni/afni-18.1.04.ebuild
+++ b/sci-biology/afni/afni-18.1.04.ebuild
@@ -11,7 +11,7 @@ SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="GPL-3+"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
RDEPEND="dev-libs/expat
^ permalink raw reply related [flat|nested] 14+ messages in thread
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