diff options
Diffstat (limited to 'sci-libs')
27 files changed, 155 insertions, 1054 deletions
diff --git a/sci-libs/bigdft-abi/ChangeLog b/sci-libs/bigdft-abi/ChangeLog index b1fc75cb5..e440a22e3 100644 --- a/sci-libs/bigdft-abi/ChangeLog +++ b/sci-libs/bigdft-abi/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*bigdft-abi-1.0.4-r2 (19 Sep 2013) + + 19 Sep 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + -bigdft-abi-1.0.4-r1.ebuild, +bigdft-abi-1.0.4-r2.ebuild: + Avoid sandbox violation when generating TeX fonts. + *bigdft-abi-1.0.4-r1 (27 Jun 2013) 27 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r1.ebuild b/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r2.ebuild index f466e9078..f466e9078 100644 --- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r1.ebuild +++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r2.ebuild diff --git a/sci-libs/bigdft/ChangeLog b/sci-libs/bigdft/ChangeLog deleted file mode 100644 index 812748003..000000000 --- a/sci-libs/bigdft/ChangeLog +++ /dev/null @@ -1,139 +0,0 @@ -# ChangeLog for sci-libs/bigdft -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> bigdft-1.7_pre12.ebuild: - Fix issue 52 - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> bigdft-1.7_pre12.ebuild: - Fix issue 52 - - 22 Feb 2013; Justin Lecher <jlec@gentoo.org> -bigdft-1.6_pre1-r4.ebuild, - bigdft-1.6.0-r2.ebuild, bigdft-1.7_pre12.ebuild, metadata.xml: - Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; - drop old - - 20 Feb 2013; Honza Macháček <Hloupy.Honza@centrum.cz> - bigdft-1.7_pre12.ebuild: - The setup of python for the compilation of the GPU support in - bigdft-1.7_pre12 improved. - - 20 Feb 2013; Honza Macháček <Hloupy.Honza@centrum.cz> - bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-GPUlink.patch: - Compilation of GPU support in bigdft-1.7_pre12 improved. Yet to be tested. - -*bigdft-1.7_pre12 (17 Jan 2013) - - 17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz> - +bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-libxc_dir_include.patch, - +files/bigdft-1.7-dev.12-nolib_mods.patch, - +files/bigdft-1.7-dev.12-tests.tar.bz2: - New version 1.7-dev.12 (1.7_pre12) from the Abinit site added; used by - sci-physics/abinit-7.0.4 but apparently segfaults it. - -*bigdft-1.6_pre1-r4 (01 Sep 2012) - - 01 Sep 2012; Honza Macháček <Hloupy.Honza@centrum.cz> - -bigdft-1.6_pre1-r3.ebuild, +bigdft-1.6_pre1-r4.ebuild, - -files/bigdft-1.6-tuto.1-GPUlibs.patch, - +files/bigdft-1.6-tuto.1-GPUlibs-1.patch, - -files/bigdft-1.6-tuto.1-bigdft.pc.patch, - +files/bigdft-1.6-tuto.1-bigdft.pc-1.patch: - Patches to install GPU support corrected not to break linking against the - compiled libraries - - 10 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz> - files/bigdft-1.6-tuto.1-GPUlibs.patch: - bigdft-1.6-tuto.1-GPUlibs.patch updated not to forget the pkg-config file - -*bigdft-1.6_pre1-r3 (04 Jul 2012) - - 04 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz> - -bigdft-1.6_pre1-r2.ebuild, +bigdft-1.6_pre1-r3.ebuild, - +files/bigdft-1.6-tuto.1-GPUlibs.patch, - +files/bigdft-1.6-tuto.1-gcc-4.6.patch: - bigdft-1.6_pre1 from -r2 to -r3: patched to install necessary libraries for - GPU support and to compile with gcc-4.6 - - 22 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> bigdft-1.6.0-r2.ebuild, - bigdft-1.6_pre1-r2.ebuild: - [sci-libs/bigdft] add ~amd64-linux - -*bigdft-1.6.0-r2 (19 Jun 2012) -*bigdft-1.6_pre1-r2 (19 Jun 2012) - - 19 Jun 2012; Honza Macháček <Hloupy.Honza@centrum.cz> - -bigdft-1.6_pre1-r1.ebuild, +bigdft-1.6_pre1-r2.ebuild, - -bigdft-1.6.0-r1.ebuild, +bigdft-1.6.0-r2.ebuild: - Reflect the split of the fortran interface out of sci-libs/netcdf - - 22 May 2012; Justin Lecher <jlec@gentoo.org> bigdft-1.6_pre1-r1.ebuild, - bigdft-1.6.0-r1.ebuild: - Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits - -*bigdft-1.6.0-r1 (15 May 2012) -*bigdft-1.6_pre1-r1 (15 May 2012) - - 15 May 2012; Honza Macháček <Hloupy.Honza@centrum.cz> - -bigdft-1.6_pre1.ebuild, +bigdft-1.6_pre1-r1.ebuild, -bigdft-1.6.0.ebuild, - +bigdft-1.6.0-r1.ebuild: - pkg-config file corrected - - 30 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz> - -bigdft-1.2.0.2.ebuild, -files/bigdft-1.2.0.2-0001.patch, - -files/bigdft-1.2.0.2-0002.patch, -files/bigdft-1.2.0.2-0003.patch, - -files/bigdft-1.2.0.2-0004.patch, -files/bigdft-1.2.0.2-testH.patch, - -bigdft-1.2.0.5.ebuild, -files/bigdft-1.2.0.5-0001.patch, - -bigdft-1.6_pre0.ebuild, -files/bigdft-1.6-tuto-bigdft.pc.patch, - -files/bigdft-1.6-tuto-libxc_dir_include.patch: - Clean-up. - -*bigdft-1.6_pre1 (22 Mar 2012) -*bigdft-1.6_pre0 (22 Mar 2012) - - 22 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz> - +bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild, +bigdft-1.6_pre0.ebuild, - +bigdft-1.6_pre1.ebuild, bigdft-1.6.0.ebuild, - +files/bigdft-1.6.0-libxc_dir_include.patch, - +files/bigdft-1.6-tuto.1-bigdft.pc.patch, - +files/bigdft-1.6-tuto.1-libxc_dir_include.patch, - +files/bigdft-1.6-tuto-bigdft.pc.patch, - +files/bigdft-1.6-tuto-libxc_dir_include.patch: - Old versions used by old versions of abinit ressurected. May be removed - forever if nobody complains about the latest abinit. 1.6.0 corrected, - 1.6_pre0 and 1.6_pre1 added; 1.6_pre1 is used by sci-physics/abinit-6.12.1. - -*bigdft-1.6.0 (18 Feb 2012) - - 18 Feb 2012; Justin Lecher <jlec@gentoo.org> -bigdft-1.2.0.2.ebuild, - -bigdft-1.2.0.5.ebuild, +bigdft-1.6.0.ebuild, metadata.xml: - Move to EAPI=4 and autotools-util.eclass - -*bigdft-1.2.0.5 (14 Dec 2011) - - 14 Dec 2011; Honza Macháček <Hloupy.Honza@centrum.cz> - bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild, - +files/bigdft-1.2.0.5-0001.patch: - Version bump to 1.2.0.5 for sci-physics/abinit-6.10.3; still not much - progress towards the current version (1.5.2 and 1.6-tuto) - - 11 Jul 2011; Honza Macháček <Hloupy.Honza@centrum.cz> - bigdft-1.2.0.2.ebuild: - The MPI support, broken by fortran-2.eclass usage, made work again. - - 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild: - Streamlined fortran-2 eclass usage - - 21 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild, - +metadata.xml: - Added fortran-2.eclass support - -*bigdft-1.2.0.2 (17 Jan 2011) - - 17 Jan 2011; Honza Macháček <Hloupy.Honza@centrum.cz> - +bigdft-1.2.0.2.ebuild, +files/bigdft-1.2.0.2-0001.patch, - +files/bigdft-1.2.0.2-0002.patch, +files/bigdft-1.2.0.2-0003.patch, - +files/bigdft-1.2.0.2-0004.patch, +files/bigdft-1.2.0.2-testH.patch: - A bigDFT ebuild for sci-physics/abinit; not the latest version but the abinit - compatible one. - diff --git a/sci-libs/bigdft/Manifest b/sci-libs/bigdft/Manifest deleted file mode 100644 index a828ad66e..000000000 --- a/sci-libs/bigdft/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST bigdft-1.6.0.tar.gz 8876759 SHA256 2d3212ef5f1ebc10fe7c627397ac6282ad41e1433ec6e66905f9d39a302913c0 SHA512 facbb78d126885dd04fed6451aa9cd1f5c755055e146cda1d2d4e90e3310fc3066b661635477db96d5b143ffaaa3ebb01107681437fd9965f3c764cf1b034361 WHIRLPOOL 97bc6c28296a92b09139e3a65266daa583011620fad5aed208e0e48627ab1d9c0ef9993d6c4c3cce5696d5c707bcdfb4b8ca7e64379909b3cf073206e32f9572 -DIST bigdft-1.7-dev.12.tar.gz 8904633 SHA256 2f899f287dd508dc616fb798cc9d01d1c79951dc68c277fb0ce19ea0ad690332 SHA512 35efe93edd7e6fb08abe919c59913c173f23e17a50104ad92e510dba5ba35ba8117012249d620896affc8acc05c9d85c6c61a411bc903750db6593456e9e8142 WHIRLPOOL 94a8d6d25fe82f3f1b89d15b4e23293d018bfb66c96fd1061a09e6352fb6811e79a15161bd3ca92e5f544253c8fa9f919d41fe069635ac07f33e21cc70878719 diff --git a/sci-libs/bigdft/bigdft-1.6.0-r2.ebuild b/sci-libs/bigdft/bigdft-1.6.0-r2.ebuild deleted file mode 100644 index e43d7e45b..000000000 --- a/sci-libs/bigdft/bigdft-1.6.0-r2.ebuild +++ /dev/null @@ -1,122 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -inherit autotools-utils eutils flag-o-matic fortran-2 toolchain-funcs - -REAL_P="${P/_pre0/-tuto}" - -DESCRIPTION="A DFT electronic structure code using a wavelet basis set" -HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/" -SRC_URI="http://inac.cea.fr/L_Sim/BigDFT/${REAL_P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux" -IUSE="cuda doc etsf_io mpi netcdf opencl test" - -RDEPEND=" - =sci-libs/libxc-1*[fortran] - virtual/blas - virtual/fortran - virtual/lapack - mpi? ( virtual/mpi ) - cuda? ( dev-util/nvidia-cuda-sdk ) - opencl? ( - || ( - dev-util/nvidia-cuda-sdk - dev-util/amdstream - ) - ) - etsf_io? ( sci-libs/etsf_io ) - netcdf? ( || ( - sci-libs/netcdf[fortran] - sci-libs/netcdf-fortran - ) - )" -DEPEND="${RDEPEND} - virtual/pkgconfig - >=sys-devel/autoconf-2.59 - doc? ( virtual/latex-base )" - -S="${WORKDIR}/${REAL_P}" - -DOCS=( README INSTALL ChangeLog AUTHORS NEWS ) - -FORTRAN_STANDARD=90 - -pkg_setup() { - # fortran-2.eclass does not handle mpi wrappers - if use mpi; then - export FC="mpif90" - export F77="mpif77" - export CC="mpicc" - else - tc-export FC F77 CC - fi - - fortran-2_pkg_setup -} - -src_prepare() { - epatch "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch - eautoreconf -} - -src_configure() { - local modules="${EPREFIX}/usr/$(get_libdir)/finclude" - local netcdff_libs="-lnetcdff" - filter-flags '-m*' '-O*' "-pipe" - local nvcflags="${CFLAGS}" -# _filter-var nvcflags '-m*' '-O*' "-pipe" - local myeconfargs=( - $(use_enable mpi) - --enable-optimised-convolution - --enable-pseudo - --enable-libbigdft - --enable-binaries - --disable-minima-hopping - --with-moduledir="${modules}" - --with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l lapack) \ - $($(tc-getPKG_CONFIG) --libs-only-l blas)" - --with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L lapack) \ - $($(tc-getPKG_CONFIG) --libs-only-L blas)" - --disable-internal-libxc - --with-libxc-path="/usr" - --with-libxc-include="${modules}" - $(use_enable cuda cuda-gpu) - $(use_with cuda cuda-path /opt/cuda) - $(use_with cuda nvcc-flags "${nvcflags}") - $(use_enable opencl) - $(use_with opencl ocl-path "${EPREFIX}/usr") - $(use_with etsf_io etsf-io) - $(use_with etsf_io etsf-io-path "${EPREFIX}/usr") - $(use_with etsf_io netcdf-path "$($(tc-getPKG_CONFIG) --libs-only-L netcdf)") - "$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")" - FCFLAGS+=" -I${modules}" - LD="$(tc-getLD)" - CPP="$(tc-getCPP)" - ) - autotools-utils_src_configure -} - -src_compile() { - #autotools-utils_src_compile() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - emake -j1 - sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc - popd > /dev/null - - use doc && autotools-utils_src_compile doc -} - -src_test() { - use test && autotools-utils_src_test -} - -src_install() { - autotools-utils_src_install HAVE_LIBXC=1 -} diff --git a/sci-libs/bigdft/bigdft-1.7_pre12.ebuild b/sci-libs/bigdft/bigdft-1.7_pre12.ebuild deleted file mode 100644 index 8ff693ea1..000000000 --- a/sci-libs/bigdft/bigdft-1.7_pre12.ebuild +++ /dev/null @@ -1,147 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -PYTHON_COMPAT=( python2_5 python2_6 python2_7 ) - -inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs - -REAL_P="${P/_pre/-dev.}" - -DESCRIPTION="A DFT electronic structure code using a wavelet basis set" -HOMEPAGE="http://inac.cea.fr/L_Sim/BigDFT/" -SRC_URI="http://forge.abinit.org/fallbacks/${REAL_P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux" -IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" - -RDEPEND=" - =sci-libs/libxc-1*[fortran] - virtual/blas - virtual/fortran - virtual/lapack - dev-libs/libyaml - mpi? ( virtual/mpi ) - cuda? ( dev-util/nvidia-cuda-sdk ) - opencl? ( - || ( - dev-util/nvidia-cuda-sdk - dev-util/amdstream - ) - ) - etsf_io? ( sci-libs/etsf_io ) - netcdf? ( || ( - sci-libs/netcdf[fortran] - sci-libs/netcdf-fortran - ) - )" -DEPEND="${RDEPEND} - virtual/pkgconfig - >=sys-devel/autoconf-2.59 - doc? ( virtual/latex-base ) - cuda? ( ${PYTHON_DEPS} ) - opencl? ( ${PYTHON_DEPS} ) - app-arch/tar - app-arch/gzip" - -S="${WORKDIR}/${REAL_P}" - -DOCS=( README INSTALL ChangeLog AUTHORS NEWS ) - -FORTRAN_STANDARD=90 - -pkg_setup() { - # fortran-2.eclass does not handle mpi wrappers - if use mpi; then - export FC="mpif90" - export F77="mpif77" - export CC="mpicc" - else - tc-export FC F77 CC - fi - - fortran-2_pkg_setup - if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then - die "Please select an openmp capable compiler like gcc[openmp]" - fi - python-any-r1_pkg_setup -} - -src_prepare() { - epatch \ - "${FILESDIR}"/"${REAL_P}"-libxc_dir_include.patch \ - "${FILESDIR}"/"${REAL_P}"-GPUlink.patch \ - "${FILESDIR}"/"${REAL_P}"-nolib_mods.patch - tar -xjf "${FILESDIR}"/"${REAL_P}"-tests.tar.bz2 -C "${S}"/tests/DFT/postSCF/ - eautoreconf -} - -src_configure() { - local openmp="" - use openmp && openmp="-fopenmp" - local modules="${EPREFIX}/usr/$(get_libdir)/finclude" - local netcdff_libs="-lnetcdff" - filter-flags '-m*' '-O*' "-pipe" - local nvcflags="${CFLAGS}" - _filter-var nvcflags '-m*' '-O*' "-pipe" - local myeconfargs=( - $(use_enable mpi) - --enable-optimised-convolution - --enable-pseudo - --enable-libbigdft - --enable-binaries - --disable-minima-hopping - --disable-internal-libyaml - --enable-internal-libabinit - --with-moduledir="${modules}" - --with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l lapack) \ - $($(tc-getPKG_CONFIG) --libs-only-l blas)" - --with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L lapack) \ - $($(tc-getPKG_CONFIG) --libs-only-L blas)" - --enable-libxc - --disable-internal-libxc - --with-libxc-include="${modules}" - $(use_enable cuda cuda-gpu) - $(use_with cuda cuda-path /opt/cuda) - $(use_with cuda nvcc-flags "${nvcflags}") - $(use_enable opencl) - $(use_with etsf_io etsf-io) - "$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")" - FCFLAGS="${FCFLAGS} ${openmp} -I${modules}" - LD="$(tc-getLD)" - CPP="$(tc-getCPP)" - ) - autotools-utils_src_configure -} - -src_compile() { - #autotools-utils_src_compile() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - emake -j1 - sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc - popd > /dev/null - - #autotools-utils_src_compile - use doc && autotools-utils_src_compile doc -} - -src_test() { - if use test; then - #autotools-utils_src_test() expanded - _check_build_dir - pushd "${BUILD_DIR}" > /dev/null || die - # Run default src_test as defined in ebuild.sh - cd tests - emake -j1 check - popd > /dev/null - fi -} - -src_install() { - autotools-utils_src_install HAVE_LIBXC=1 -} diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch deleted file mode 100644 index 386e39dc7..000000000 --- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-GPUlibs-1.patch +++ /dev/null @@ -1,26 +0,0 @@ -diff -Naur orig/bigdft-1.6-tuto.1.orig/src/CUDA/Makefile.am patched/bigdft-1.6-tuto.1/src/CUDA/Makefile.am ---- bigdft-1.6-tuto.1.orig/src/CUDA/Makefile.am 2011-09-27 12:43:06.000000000 +0000 -+++ bigdft-1.6-tuto.1/src/CUDA/Makefile.am 2012-07-04 12:08:27.000000000 +0000 -@@ -43,7 +43,8 @@ - # Not used anymore, to be removed - #INC_CUDA = -I@LIB_CUTIL_PATH@ - EXTRA_PROGRAMS = conv_check --noinst_LIBRARIES = libGPU.a libbasef.a -+lib_LIBRARIES = libGPU.a -+noinst_LIBRARIES = libbasef.a - - libGPU_a_SOURCES = $(SOURCES_CU_CONV1) $(SOURCES_SHARED) $(SOURCES_CONV) - AM_CPPFLAGS = $(INC_CUDA) -I. -I$(top_builddir) -I@CUDA_PATH@/include/ @LIBSGPU_INCLUDE@ -DCUBLAS_USE_THUNKING -diff -Naur orig/bigdft-1.6-tuto.1.orig/src/OpenCL/Makefile.am patched/bigdft-1.6-tuto.1/src/OpenCL/Makefile.am ---- bigdft-1.6-tuto.1.orig/src/OpenCL/Makefile.am 2011-09-27 12:43:06.000000000 +0000 -+++ bigdft-1.6-tuto.1/src/OpenCL/Makefile.am 2012-07-04 12:09:02.000000000 +0000 -@@ -26,7 +26,8 @@ - - EXTRA_PROGRAMS = conv_check conv_check_fft bench_conv bench_conv_quick bench_zgemm stream_check - --noinst_LIBRARIES = libbasef.a libbasec.a libOCL.a libStream.a -+lib_LIBRARIES = libOCL.a -+noinst_LIBRARIES = libbasef.a libbasec.a libStream.a - - libbasef_a_SOURCES = $(mpi_source) - libbasef_a_LIBADD = ../modules/defs.o ../modules/base.o \ diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch deleted file mode 100644 index 7c3380a9b..000000000 --- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-bigdft.pc-1.patch +++ /dev/null @@ -1,207 +0,0 @@ -diff -Naur bigdft-1.6-tuto_orig/Makefile.am bigdft-1.6-tuto/Makefile.am ---- Makefile.am 2011-10-18 07:39:52.000000000 +0000 -+++ Makefile.am 2012-03-21 10:08:44.000000000 +0000 -@@ -4,7 +4,10 @@ - - ACLOCAL_AMFLAGS = -I config/m4 - --DISTCLEANFILES = config.inc -+DISTCLEANFILES = config.inc bigdft.pc -+ -+pkgconfigdir = $(libdir)/pkgconfig -+pkgconfig_DATA = bigdft.pc - - if BUILD_LIBABINIT - libABINIT_dir = libABINIT/src -diff -Naur bigdft-1.6-tuto_orig/Makefile.in bigdft-1.6-tuto/Makefile.in ---- Makefile.in 2012-03-21 10:03:28.000000000 +0000 -+++ Makefile.in 2012-03-21 10:20:48.000000000 +0000 -@@ -33,7 +33,7 @@ - POST_UNINSTALL = : - subdir = . - DIST_COMMON = README $(am__configure_deps) $(srcdir)/Makefile.am \ -- $(srcdir)/Makefile.in $(srcdir)/config.h.in \ -+ $(srcdir)/Makefile.in $(srcdir)/bigdft.pc.in $(srcdir)/config.h.in \ - $(top_srcdir)/config/Doxyfile.in $(top_srcdir)/configure \ - AUTHORS COPYING ChangeLog INSTALL NEWS config/depcomp \ - config/install-sh config/missing -@@ -48,7 +48,7 @@ - configure.lineno config.status.lineno - mkinstalldirs = $(install_sh) -d - CONFIG_HEADER = config.h --CONFIG_CLEAN_FILES = config/Doxyfile -+CONFIG_CLEAN_FILES = bigdft.pc config/Doxyfile - CONFIG_CLEAN_VPATH_FILES = - SOURCES = - DIST_SOURCES = -@@ -59,6 +59,35 @@ - install-pdf-recursive install-ps-recursive install-recursive \ - installcheck-recursive installdirs-recursive pdf-recursive \ - ps-recursive uninstall-recursive -+am__vpath_adj_setup = srcdirstrip=`echo "$(srcdir)" | sed 's|.|.|g'`; -+am__vpath_adj = case $$p in \ -+ $(srcdir)/*) f=`echo "$$p" | sed "s|^$$srcdirstrip/||"`;; \ -+ *) f=$$p;; \ -+ esac; -+am__strip_dir = f=`echo $$p | sed -e 's|^.*/||'`; -+am__install_max = 40 -+am__nobase_strip_setup = \ -+ srcdirstrip=`echo "$(srcdir)" | sed 's/[].[^$$\\*|]/\\\\&/g'` -+am__nobase_strip = \ -+ for p in $$list; do echo "$$p"; done | sed -e "s|$$srcdirstrip/||" -+am__nobase_list = $(am__nobase_strip_setup); \ -+ for p in $$list; do echo "$$p $$p"; done | \ -+ sed "s| $$srcdirstrip/| |;"' / .*\//!s/ .*/ ./; s,\( .*\)/[^/]*$$,\1,' | \ -+ $(AWK) 'BEGIN { files["."] = "" } { files[$$2] = files[$$2] " " $$1; \ -+ if (++n[$$2] == $(am__install_max)) \ -+ { print $$2, files[$$2]; n[$$2] = 0; files[$$2] = "" } } \ -+ END { for (dir in files) print dir, files[dir] }' -+am__base_list = \ -+ sed '$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;$$!N;s/\n/ /g' | \ -+ sed '$$!N;$$!N;$$!N;$$!N;s/\n/ /g' -+am__uninstall_files_from_dir = { \ -+ test -z "$$files" \ -+ || { test ! -d "$$dir" && test ! -f "$$dir" && test ! -r "$$dir"; } \ -+ || { echo " ( cd '$$dir' && rm -f" $$files ")"; \ -+ $(am__cd) "$$dir" && rm -f $$files; }; \ -+ } -+am__installdirs = "$(DESTDIR)$(pkgconfigdir)" -+DATA = $(pkgconfig_DATA) - RECURSIVE_CLEAN_TARGETS = mostlyclean-recursive clean-recursive \ - distclean-recursive maintainer-clean-recursive - AM_RECURSIVE_TARGETS = $(RECURSIVE_TARGETS:-recursive=) \ -@@ -232,7 +261,9 @@ - config/m4 - - ACLOCAL_AMFLAGS = -I config/m4 --DISTCLEANFILES = config.inc -+DISTCLEANFILES = config.inc bigdft.pc -+pkgconfigdir = $(libdir)/pkgconfig -+pkgconfig_DATA = bigdft.pc - @BUILD_LIBABINIT_FALSE@libABINIT_dir = - @BUILD_LIBABINIT_TRUE@libABINIT_dir = libABINIT/src - @BUILD_LIBXC_FALSE@libXC_dir = -@@ -307,8 +338,28 @@ - - distclean-hdr: - -rm -f config.h stamp-h1 -+bigdft.pc: $(top_builddir)/config.status $(srcdir)/bigdft.pc.in -+ cd $(top_builddir) && $(SHELL) ./config.status $@ - config/Doxyfile: $(top_builddir)/config.status $(top_srcdir)/config/Doxyfile.in - cd $(top_builddir) && $(SHELL) ./config.status $@ -+install-pkgconfigDATA: $(pkgconfig_DATA) -+ @$(NORMAL_INSTALL) -+ test -z "$(pkgconfigdir)" || $(MKDIR_P) "$(DESTDIR)$(pkgconfigdir)" -+ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \ -+ for p in $$list; do \ -+ if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \ -+ echo "$$d$$p"; \ -+ done | $(am__base_list) | \ -+ while read files; do \ -+ echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(pkgconfigdir)'"; \ -+ $(INSTALL_DATA) $$files "$(DESTDIR)$(pkgconfigdir)" || exit $$?; \ -+ done -+ -+uninstall-pkgconfigDATA: -+ @$(NORMAL_UNINSTALL) -+ @list='$(pkgconfig_DATA)'; test -n "$(pkgconfigdir)" || list=; \ -+ files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \ -+ dir='$(DESTDIR)$(pkgconfigdir)'; $(am__uninstall_files_from_dir) - - # This directory's subdirectories are mostly independent; you can cd - # into them and run `make' without going through this Makefile. -@@ -622,9 +673,12 @@ - exit 1; } >&2 - check-am: all-am - check: check-recursive --all-am: Makefile config.h -+all-am: Makefile $(DATA) config.h - installdirs: installdirs-recursive - installdirs-am: -+ for dir in "$(DESTDIR)$(pkgconfigdir)"; do \ -+ test -z "$$dir" || $(MKDIR_P) "$$dir"; \ -+ done - install: install-recursive - install-exec: install-exec-recursive - install-data: install-data-recursive -@@ -672,7 +726,7 @@ - - info-am: - --install-data-am: -+install-data-am: install-pkgconfigDATA - - install-dvi: install-dvi-recursive - -@@ -718,7 +772,7 @@ - - ps-am: - --uninstall-am: -+uninstall-am: uninstall-pkgconfigDATA - - .MAKE: $(RECURSIVE_CLEAN_TARGETS) $(RECURSIVE_TARGETS) all \ - ctags-recursive install-am install-strip tags-recursive -@@ -733,10 +787,10 @@ - install-data-am install-dvi install-dvi-am install-exec \ - install-exec-am install-html install-html-am install-info \ - install-info-am install-man install-pdf install-pdf-am \ -- install-ps install-ps-am install-strip installcheck \ -+ install-pkgconfigDATA install-ps install-ps-am install-strip installcheck \ - installcheck-am installdirs installdirs-am maintainer-clean \ - maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ -- pdf-am ps ps-am tags tags-recursive uninstall uninstall-am -+ pdf-am ps ps-am tags tags-recursive uninstall uninstall-am uninstall-pkgconfigDATA - - configure - -diff -Naur bigdft-1.6-tuto_orig/bigdft.pc.in bigdft-1.6-tuto/bigdft.pc.in ---- bigdft.pc.in 1970-01-01 00:00:00.000000000 +0000 -+++ bigdft.pc.in 2012-02-01 09:43:59.000000000 +0000 -@@ -0,0 +1,15 @@ -+@USE_CUDA_GPU_FALSE@libs_cuda= -+@USE_CUDA_GPU_TRUE@libs_cuda=$(top_builddir)/src/CUDA/libGPU.a -+@USE_OCL_FALSE@libs_ocl= -+@USE_OCL_TRUE@libs_ocl=$(top_builddir)/src/OpenCL/libOCL.a -lstdc++ -+prefix=@prefix@ -+exec_prefix=@exec_prefix@ -+libdir=@libdir@ -+includedir=@includedir@ -+ -+Name: libbigdft -+Description: Library for DFT calculation over wavelets. -+Requires: -+Version: @VERSION@ -+Libs: -L${libdir} -lbigdft -lpoissonsolver ${libs_cuda} ${libs_ocl} @LIBS@ @FCLIBS@ -+Cflags: -I${includedir} -diff -Naur bigdft-1.6-tuto_orig/configure bigdft-1.6-tuto/configure ---- configure 2012-03-21 10:03:26.000000000 +0000 -+++ configure 2012-03-21 11:04:52.000000000 +0000 -@@ -8512,7 +8512,7 @@ - docdir="${docdir}" - - --ac_config_files="$ac_config_files Makefile libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile" -+ac_config_files="$ac_config_files Makefile bigdft.pc libABINIT/src/Makefile config/Doxyfile src/Makefile src/modules/Makefile src/modules/configure.inc src/profiling/Makefile src/PSolver/Makefile src/convolutions/Makefile src/CUDA/Makefile src/OpenCL/Makefile src/dgemmsy/Makefile src/convolutions-c/Makefile src/art/Makefile src/tools/Makefile src/tools/bader/Makefile utils/Makefile utils/PSPfiles/Makefile pseudo/Makefile pseudo/src/Makefile pseudo/tests/Makefile doc/Makefile tests/Makefile tests/fft/Makefile tests/PSolver/Makefile tests/H2-freq/Makefile tests/MINHOP/Makefile tests/NEB/Makefile tests/NEB/input tests/NEB/NEB_include.sh tests/XabsCheb/Makefile tests/SPLSAD/Makefile tests/TDDFT/Makefile tests/OP2P/Makefile tests/DFT/Makefile tests/OpenCL/Makefile tests/CUDA/Makefile tests/ETSF_IO/Makefile tests/tutorials/Makefile tests/xc/Makefile" - - - # Call libXC ./configure script recursively. -@@ -9349,6 +9349,7 @@ - "config.h") CONFIG_HEADERS="$CONFIG_HEADERS config.h" ;; - "depfiles") CONFIG_COMMANDS="$CONFIG_COMMANDS depfiles" ;; - "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;; -+ "bigdft.pc") CONFIG_FILES="$CONFIG_FILES bigdft.pc" ;; - "libABINIT/src/Makefile") CONFIG_FILES="$CONFIG_FILES libABINIT/src/Makefile" ;; - "config/Doxyfile") CONFIG_FILES="$CONFIG_FILES config/Doxyfile" ;; - "src/Makefile") CONFIG_FILES="$CONFIG_FILES src/Makefile" ;; -diff -Naur bigdft-1.6-tuto_orig/configure.ac bigdft-1.6-tuto/configure.ac ---- configure.ac 2012-03-21 10:03:02.000000000 +0000 -+++ configure.ac 2012-03-21 10:48:53.000000000 +0000 -@@ -715,6 +715,7 @@ - dnl Give the name of file.in to transform to file - AC_CONFIG_FILES([ - Makefile -+bigdft.pc - libABINIT/src/Makefile - config/Doxyfile - src/Makefile diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch deleted file mode 100644 index e89da2546..000000000 --- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-gcc-4.6.patch +++ /dev/null @@ -1,67 +0,0 @@ -diff -Naurp bigdft-1.6-tuto.1.orig/src/art/art_lanczos.f90 bigdft-1.6-tuto.1/src/art/art_lanczos.f90 ---- bigdft-1.6-tuto.1.orig/src/art/art_lanczos.f90 2011-10-17 08:46:50.000000000 +0000 -+++ bigdft-1.6-tuto.1/src/art/art_lanczos.f90 2012-06-22 13:03:49.000000000 +0000 -@@ -80,11 +80,30 @@ subroutine lanczos( maxvec, new_projecti - integer :: i_min - real(kind=8) :: e_min - !_______________________ -+ -+ interface -+ !> ART center -+ !! @author -+ !! Written by EM 2010, see ~/AUTHORS -+ !! It places the center of mass of a 3D vector at (0,0,0). -+ subroutine center( vector, vecsize ) -+ -+ use defs, only : natoms, constr -+ use bigdft_forces, only : in_system -+ implicit none -+ -+ !Arguments -+ integer, intent(in) :: vecsize -+ real(kind=8), dimension(vecsize), intent(inout), target :: vector -+ -+ end subroutine center -+ end interface -+ - newpos = 0.0d0 - diag = 0.0d0 - offdiag = 0.0d0 - lanc = 0.0d0 -- -+ - boxl = box * scala - ! We now take the current position as the - ! reference point and will make a displacement -diff -Naurp bigdft-1.6-tuto.1.orig/src/art/calcfo_sw.f90 bigdft-1.6-tuto.1/src/art/calcfo_sw.f90 ---- bigdft-1.6-tuto.1.orig/src/art/calcfo_sw.f90 2011-10-17 08:46:50.000000000 +0000 -+++ bigdft-1.6-tuto.1/src/art/calcfo_sw.f90 2012-06-22 12:58:35.000000000 +0000 -@@ -475,6 +475,28 @@ function diff_square_force_one(P,numnei, - integer :: trash_evalf - real(8), dimension(3*natoms,configs_to_fit) :: force_tempo,tmp_force - -+interface -+! subroutine to compute forces of one atom -+subroutine SWcalczone(nat,posa,boxl,tmp_force, this_atom,numnei,nei) -+ -+ -+ use SWpotential -+ use defs, only : boundary,maxnei,iproc,MPI_COMM_WORLD -+ -+ implicit none -+ -+ integer, intent(in) :: nat -+ real(kind=8), intent(in), dimension(3*nat) :: posa -+ real(kind=8), dimension(3), intent(inout) :: boxl -+ integer, intent(in) :: this_atom -+ real(8), intent(out), dimension(3*nat), target:: tmp_force -+ -+ -+ integer, dimension(nat),intent(in) :: numnei -+ integer, dimension(nat,maxnei),intent(in) :: nei -+end subroutine SWcalczone -+end interface -+ - trash_evalf = 0 - my_counter = 0 - force_tempo = force_work_fit diff --git a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch deleted file mode 100644 index 6d0f6046a..000000000 --- a/sci-libs/bigdft/files/bigdft-1.6-tuto.1-libxc_dir_include.patch +++ /dev/null @@ -1,50 +0,0 @@ ---- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000 -+++ configure.ac 2011-11-23 14:09:19.000000000 +0000 -@@ -551,14 +551,17 @@ - ac_build_libxc="no" - AC_ARG_ENABLE(libxc, AS_HELP_STRING([--disable-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes") - AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes") --AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]), -+AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]), - ac_libxc_dir=$withval, ac_libxc_dir=) -+AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]), -+ ac_libxc_dir_include=$withval, ac_libxc_dir_include=) - if test x"$ac_use_libxc" = x"yes" ; then - ac_build_libxc=$ac_internal_libxc - if test "$ac_internal_libxc" = "yes" ; then - ac_build_libxc="yes" - ac_use_libxc="yes" - ac_libxc_dir="$top_builddir"/libxc-1.1.0/src -+ ac_libxc_dir_include="$ac_libxc_dir"/include - AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src) - AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src) - LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs" -@@ -566,6 +569,9 @@ - else - if test -n "$ac_libxc_dir" ; then - LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib" -+ if test x"$ac_libxc_dir_include" = x ; then -+ ac_libxc_dir_include="$ac_libxc_dir"/include -+ fi - - dnl Test the given implementation of libXC. - ac_libxc_libname="xc" -@@ -574,13 +580,13 @@ - ac_libxc_libname="dft_xc" - AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no) - fi -- AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no") -- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no") -- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$capitalize_module_ext, funcs="yes", funcs="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$capitalize_module_ext, lib="yes", lib="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$capitalize_module_ext, types="yes", types="no") - if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then - ac_use_libxc="yes" -- AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include) -- AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include) -+ AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include) -+ AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include) - LIBXC_LIBS="-l"$ac_libxc_libname - fi - else diff --git a/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch deleted file mode 100644 index 7179fcb0f..000000000 --- a/sci-libs/bigdft/files/bigdft-1.6.0-libxc_dir_include.patch +++ /dev/null @@ -1,50 +0,0 @@ ---- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000 -+++ configure.ac 2011-11-23 14:09:19.000000000 +0000 -@@ -604,14 +604,17 @@ - ac_build_libxc="no" - AC_ARG_WITH(libxc, AS_HELP_STRING([--without-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes") - AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes") --AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]), -+AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]), - ac_libxc_dir=$withval, ac_libxc_dir=) -+AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]), -+ ac_libxc_dir_include=$withval, ac_libxc_dir_include=) - if test x"$ac_use_libxc" = x"yes" ; then - ac_build_libxc=$ac_internal_libxc - if test "$ac_internal_libxc" = "yes" ; then - ac_build_libxc="yes" - ac_use_libxc="yes" - ac_libxc_dir="$top_builddir"/libxc-1.1.0/src -+ ac_libxc_dir_include="$ac_libxc_dir"/include - AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src) - AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src) - LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs" -@@ -619,6 +622,9 @@ - else - if test -n "$ac_libxc_dir" ; then - LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib" -+ if test x"$ac_libxc_dir_include" = x ; then -+ ac_libxc_dir_include="$ac_libxc_dir"/include -+ fi - - dnl Test the given implementation of libXC. - ac_libxc_libname="xc" -@@ -587,13 +593,13 @@ - ac_libxc_libname="dft_xc" - AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no) - fi -- AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no") -- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no") -- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no") - if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then - ac_use_libxc="yes" -- AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include) -- AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include) -+ AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include) -+ AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include) - LIBXC_LIBS="-l"$ac_libxc_libname - fi - else diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-GPUlink.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-GPUlink.patch deleted file mode 100644 index f4b0e18a9..000000000 --- a/sci-libs/bigdft/files/bigdft-1.7-dev.12-GPUlink.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naurp bigdft-1.7-dev.12.orig/S_GPU/src/Makefile.in bigdft-1.7-dev.12/S_GPU/src/Makefile.in ---- bigdft-1.7-dev.12.orig/S_GPU/src/Makefile.in 2012-07-16 08:24:00.000000000 +0000 -+++ bigdft-1.7-dev.12/S_GPU/src/Makefile.in 2013-02-19 15:59:06.142835878 +0000 -@@ -88,7 +88,7 @@ am__objects_1 = libs_gpu_la-s_gpu_C.lo \ - libs_gpu_la-s_gpu_F.lo - am_libs_gpu_la_OBJECTS = $(am__objects_1) - libs_gpu_la_OBJECTS = $(am_libs_gpu_la_OBJECTS) --libs_gpu_la_LINK = $(LIBTOOL) --tag=CXX $(libs_gpu_la_LIBTOOLFLAGS) \ -+libs_gpu_la_LINK = $(LIBTOOL) --tag=CXX $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CXXLD) $(AM_CXXFLAGS) \ - $(CXXFLAGS) $(libs_gpu_la_LDFLAGS) $(LDFLAGS) -o $@ - DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch deleted file mode 100644 index 9084d08e5..000000000 --- a/sci-libs/bigdft/files/bigdft-1.7-dev.12-libxc_dir_include.patch +++ /dev/null @@ -1,50 +0,0 @@ ---- configure.ac.orig 2011-11-23 14:02:15.000000000 +0000 -+++ configure.ac 2011-11-23 14:09:19.000000000 +0000 -@@ -743,14 +743,17 @@ - ac_build_libxc="no" - AC_ARG_ENABLE(libxc, AS_HELP_STRING([--without-libxc], [Do not link with libXC library (default = yes).]), ac_use_libxc=$enableval, ac_use_libxc="yes") - AC_ARG_ENABLE(internal-libxc, AS_HELP_STRING([--disable-internal-libxc], [Do not build and link with internal libXC library (default = yes).]), ac_internal_libxc=$enableval, ac_internal_libxc="yes") --AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib and module files (default = None).]), -+AC_ARG_WITH(libxc-path, AS_HELP_STRING([--with-libxc-path], [Give the path for an external libXC library, lib files (default = None).]), - ac_libxc_dir=$withval, ac_libxc_dir=) -+AC_ARG_WITH(libxc-include, AS_HELP_STRING([--with-libxc-include], [Give the path for an external libXC library module files (default = None).]), -+ ac_libxc_dir_include=$withval, ac_libxc_dir_include=) - if test x"$ac_use_libxc" = x"yes" ; then - ac_build_libxc=$ac_internal_libxc - if test "$ac_internal_libxc" = "yes" ; then - ac_build_libxc="yes" - ac_use_libxc="yes" - ac_libxc_dir="$top_builddir"/libxc-1.1.0/src -+ ac_libxc_dir_include="$ac_libxc_dir"/include - AC_SUBST(LIBXC_DIR, "\$(top_builddir)"/libxc-1.1.0/src) - AC_SUBST(LIBXC_INCLUDE, "-I\$(top_builddir)"/libxc-1.1.0/src) - LDFLAGS="$LDFLAGS -L\$(top_builddir)/libxc-1.1.0/src/.libs" -@@ -758,6 +761,9 @@ - else - if test -n "$ac_libxc_dir" ; then - LDFLAGS="$LDFLAGS -L$ac_libxc_dir/lib" -+ if test x"$ac_libxc_dir_include" = x ; then -+ ac_libxc_dir_include="$ac_libxc_dir"/include -+ fi - - dnl Test the given implementation of libXC. - ac_libxc_libname="xc" -@@ -766,13 +772,13 @@ - ac_libxc_libname="dft_xc" - AC_CHECK_LIB($ac_libxc_libname, xc_f90_lda_vxc, withlibxc=yes, withlibxc=no) - fi -- AC_CHECK_FILE($ac_libxc_dir/include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no") -- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no") -- AC_CHECK_FILE($ac_libxc_dir/include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/libxc_funcs_m.$ax_fc_mod_ext, funcs="yes", funcs="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_lib_m.$ax_fc_mod_ext, lib="yes", lib="no") -+ AC_CHECK_FILE($ac_libxc_dir_include/xc_f90_types_m.$ax_fc_mod_ext, types="yes", types="no") - if test "$withlibxc" = "yes" -a "$funcs" = "yes" -a "$lib" = "yes" -a "$types" = "yes"; then - ac_use_libxc="yes" -- AC_SUBST(LIBXC_DIR, $ac_libxc_dir/include) -- AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir/include) -+ AC_SUBST(LIBXC_DIR, $ac_libxc_dir_include) -+ AC_SUBST(LIBXC_INCLUDE, "-I"$ac_libxc_dir_include) - LIBXC_LIBS="-l"$ac_libxc_libname - fi - else diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch b/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch deleted file mode 100644 index 8137a48ab..000000000 --- a/sci-libs/bigdft/files/bigdft-1.7-dev.12-nolib_mods.patch +++ /dev/null @@ -1,25 +0,0 @@ -diff -Naurp bigdft-1.7-dev.12.orig/src/Makefile.am bigdft-1.7-dev.12/src/Makefile.am ---- bigdft-1.7-dev.12.orig/src/Makefile.am 2012-07-16 07:46:11.000000000 +0000 -+++ bigdft-1.7-dev.12/src/Makefile.am 2013-01-09 14:09:58.198905489 +0000 -@@ -45,6 +45,9 @@ EXTRA_DIST = \ - # ------------- - if BUILD_LIB_BIGDFT - lib_bigdft = libbigdft.a libdft_common.a -+else -+lib_bigdft = -+endif - PS_SOURCES = PSolver/Build_Kernel.f90 \ - PSolver/xcenergy.f90 \ - PSolver/3Dgradient.f90 \ -@@ -53,11 +56,6 @@ PS_SOURCES = PSolver/Build_Kernel.f90 \ - PSolver/wofz.f90 \ - lib/fft/fft3d.f90 - PS_MODULES = PSolver/Poisson_Solver.f90 --else --lib_bigdft = --PS_SOURCES = --PS_MODULES = --endif - if BUILD_BINARIES - binaries_sources = bigdft memguess splsad NEB frequencies MDanalysis $(minima_hopping_sources) bart abscalc BigDFT2Wannier WaCo - local_binaries = test_forces diff --git a/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2 b/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2 Binary files differdeleted file mode 100644 index d74c56176..000000000 --- a/sci-libs/bigdft/files/bigdft-1.7-dev.12-tests.tar.bz2 +++ /dev/null diff --git a/sci-libs/bigdft/metadata.xml b/sci-libs/bigdft/metadata.xml deleted file mode 100644 index fcc220851..000000000 --- a/sci-libs/bigdft/metadata.xml +++ /dev/null @@ -1,10 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -<use> - <flag name="cuda">Add cuda support</flag> - <flag name="etsf_io">Undocumented USE</flag> - <flag name="opencl">Undocumented USE</flag> -</use> -</pkgmetadata> diff --git a/sci-libs/modglue/ChangeLog b/sci-libs/modglue/ChangeLog index bc9c7e433..36095f3ef 100644 --- a/sci-libs/modglue/ChangeLog +++ b/sci-libs/modglue/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 19 Sep 2013; François Bissey <francois.bissey@canterbury.ac.nz> + +files/modglue-1.19-Makefiles.patch, -files/modglue-1.16-lib64.patch, + -files/modglue-1.19-ldflags.patch, -files/modglue-1.19-parallelmake.patch, + modglue-1.19.ebuild: + Fixing sandbox violations + *modglue-1.19 (18 Sep 2013) 18 Sep 2013; François Bissey <francois.bissey@canterbury.ac.nz> diff --git a/sci-libs/modglue/files/modglue-1.16-lib64.patch b/sci-libs/modglue/files/modglue-1.16-lib64.patch deleted file mode 100644 index e67adba2e..000000000 --- a/sci-libs/modglue/files/modglue-1.16-lib64.patch +++ /dev/null @@ -1,61 +0,0 @@ ---- Makefile.in.orig 2010-03-04 10:34:54.000000000 +1300 -+++ Makefile.in 2010-08-23 23:21:34.931886424 +1200 -@@ -3,6 +3,9 @@ - - .PHONY: all install library static examples uninstall clean distclean - -+prefix = @prefix@ -+exec_prefix = @exec_prefix@ -+ - all: library - #examples - -@@ -17,8 +20,8 @@ - - install: - ( cd src && $(MAKE) install ); -- @INSTALL@ -d -m 755 ${DESTDIR}@prefix@/@libdir@/pkgconfig -- @INSTALL@ -m 644 modglue.pc ${DESTDIR}@prefix@/@libdir@/pkgconfig/ -+ @INSTALL@ -d -m 755 ${DESTDIR}@libdir@/pkgconfig -+ @INSTALL@ -m 644 modglue.pc ${DESTDIR}@libdir@/pkgconfig/ - @INSTALL@ -d -m 755 ${DESTDIR}@prefix@/share/man/man1 - @INSTALL@ man/man1/prompt.1 ${DESTDIR}@prefix@/share/man/man1 - @INSTALL@ man/man1/ptywrap.1 ${DESTDIR}@prefix@/share/man/man1 ---- src/Makefile.in.orig 2010-03-04 10:34:54.000000000 +1300 -+++ src/Makefile.in 2010-08-23 23:21:41.165883457 +1200 -@@ -1,6 +1,8 @@ - - - MACTEST= @MAC_OS_X@ -+prefix = @prefix@ -+exec_prefix = @exec_prefix@ - - ifeq ($(strip $(MACTEST)),) - LIBTOOL = libtool -@@ -18,7 +20,7 @@ - LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @prefix@/@libdir@ @LIBS@ - MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ - IPHASE = ${LIBTOOL} --mode=install @INSTALL@ --FPHASE = ${LIBTOOL} --mode=finish @prefix@/@libdir@ -+FPHASE = ${LIBTOOL} --mode=finish @libdir@ - - TIMESTAMP = -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\" - -@@ -98,13 +100,13 @@ - - install: library tools - @INSTALL@ -m 755 -d ${DESTDIR}@prefix@ -- @INSTALL@ -m 755 -d ${DESTDIR}@prefix@/@libdir@ -- @INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/@libdir@ -+ @INSTALL@ -m 755 -d ${DESTDIR}@libdir@ -+ @INSTALL@ -m 755 -d ${DEVDESTDIR}@libdir@ - @INSTALL@ -m 755 -d ${DESTDIR}@prefix@/bin - @INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/include/modglue -- ${IPHASE} libmodglue.la ${DESTDIR}@prefix@/@libdir@ -+ ${IPHASE} libmodglue.la ${DESTDIR}@libdir@ - ifneq ($(DESTDIR),$(DEVDESTDIR)) -- mv ${DESTDIR}@prefix@/@libdir@/libmodglue*.so ${DEVDESTDIR}@prefix@/@libdir@ -+ mv ${DESTDIR}@libdir@/libmodglue*.so ${DEVDESTDIR}@libdir@ - endif - # ${IPHASE} libmid.la ${DESTDIR}@prefix@/lib - ${FPHASE} diff --git a/sci-libs/modglue/files/modglue-1.19-Makefiles.patch b/sci-libs/modglue/files/modglue-1.19-Makefiles.patch new file mode 100644 index 000000000..a1dae99f0 --- /dev/null +++ b/sci-libs/modglue/files/modglue-1.19-Makefiles.patch @@ -0,0 +1,113 @@ +--- Makefile.in.orig 2013-02-24 11:18:44.000000000 +1300 ++++ Makefile.in 2013-09-20 10:05:25.316018672 +1200 +@@ -3,12 +3,15 @@ + + .PHONY: all install library static examples uninstall clean distclean + ++prefix = @prefix@ ++exec_prefix = @exec_prefix@ ++ + all: library + #examples + + library: + echo @libdir@ +- ( cd src && $(MAKE) ); ++ ( cd src $(MAKE) library tools ); + + static: + ( cd src && $(MAKE) static ); +@@ -18,8 +21,8 @@ + + install: + ( cd src && $(MAKE) install ); +- @INSTALL@ -d -m 755 ${DESTDIR}@prefix@/@libdir@/pkgconfig +- @INSTALL@ -m 644 modglue.pc ${DESTDIR}@prefix@/@libdir@/pkgconfig/ ++ @INSTALL@ -d -m 755 ${DESTDIR}@libdir@/pkgconfig ++ @INSTALL@ -m 644 modglue.pc ${DESTDIR}@libdir@/pkgconfig/ + @INSTALL@ -d -m 755 ${DESTDIR}@prefix@/share/man/man1 + @INSTALL@ man/man1/prompt.1 ${DESTDIR}@prefix@/share/man/man1 + @INSTALL@ man/man1/ptywrap.1 ${DESTDIR}@prefix@/share/man/man1 +--- src/Makefile.in.orig 2013-02-24 11:18:44.000000000 +1300 ++++ src/Makefile.in 2013-09-20 10:07:56.956164930 +1200 +@@ -1,6 +1,8 @@ + + + MACTEST= @MAC_OS_X@ ++prefix = @prefix@ ++exec_prefix = @exec_prefix@ + + ifeq ($(strip $(MACTEST)),) + LIBTOOL = libtool +@@ -21,11 +23,11 @@ + LTRELEASE = `echo ${RELEASE} | sed -e "s/\./:/g"` + + CPHASE = ${LIBTOOL} --tag=CXX --mode=compile @CXX@ -c @CFLAGS@ +-LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @prefix@@libdir@ @LIBS@ ++LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @libdir@ @LIBS@ + #LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} @LIBS@ + MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ + IPHASE = ${LIBTOOL} --mode=install @INSTALL@ +-FPHASE = ${LIBTOOL} --mode=finish @prefix@/@libdir@ ++FPHASE = ${LIBTOOL} --mode=finish ${DESTDIR}@libdir@ + + TIMESTAMP = -D"DATETIME=\"`date | sed -e 's/ / /'`\"" -DHOSTNAME=\"`hostname`\" + +@@ -56,21 +58,21 @@ + + #------- Tests ---------------------------------------- + +-test_child_process: test_child_process.o ++test_child_process: library test_child_process.o + ${MPHASE} -o test_child_process $< libmodglue.la + +-test_ext_process: test_ext_process.o ++test_ext_process: library test_ext_process.o + ${MPHASE} -o test_ext_process $< libmodglue.la + +-test_pipe: test_pipe.o ++test_pipe: library test_pipe.o + ${MPHASE} -o test_pipe $< libmodglue.la + +-test_writes: test_writes.o ++test_writes: library test_writes.o + ${MPHASE} -o test_writes $< libmodglue.la + + #------- Tools ---------------------------------------- + +-prompt: prompt.o ++prompt: library prompt.o + ${MPHASE} -o prompt prompt.o `pkg-config sigc++-2.0 --libs` libmodglue.la + # chrpath -d .libs/prompt + +@@ -85,10 +87,10 @@ + endif + + +-ptywrap: ptywrap.o ++ptywrap: library ptywrap.o + ${MPHASE} -o ptywrap ptywrap.o @LINK_UTIL@ + +-ptywrap_static: ptywrap.o ++ptywrap_static: library ptywrap.o + ${CPHASE} ${TIMESTAMP} -o ptywrap.o \ + -I@top_srcdir@/include -DSTATICBUILD ptywrap.cc + ifeq ($(strip $(MACTEST)),) +@@ -109,13 +111,13 @@ + DEVDESTDIR=${DESTDIR} + endif + @INSTALL@ -m 755 -d ${DESTDIR}@prefix@ +- @INSTALL@ -m 755 -d ${DESTDIR}@prefix@/@libdir@ +- @INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/@libdir@ ++ @INSTALL@ -m 755 -d ${DESTDIR}@libdir@ ++ @INSTALL@ -m 755 -d ${DEVDESTDIR}@libdir@ + @INSTALL@ -m 755 -d ${DESTDIR}@prefix@/bin + @INSTALL@ -m 755 -d ${DEVDESTDIR}@prefix@/include/modglue +- ${IPHASE} libmodglue.la ${DESTDIR}@prefix@/@libdir@ ++ ${IPHASE} libmodglue.la ${DESTDIR}@libdir@ + ifneq ($(DESTDIR),$(DEVDESTDIR)) +- mv ${DESTDIR}@prefix@/@libdir@/libmodglue*.so ${DEVDESTDIR}@prefix@/@libdir@ ++ mv ${DESTDIR}@libdir@/libmodglue*.so ${DEVDESTDIR}@libdir@ + endif + # ${IPHASE} libmid.la ${DESTDIR}@prefix@/lib + ${FPHASE} diff --git a/sci-libs/modglue/files/modglue-1.19-ldflags.patch b/sci-libs/modglue/files/modglue-1.19-ldflags.patch deleted file mode 100644 index a564d4fb2..000000000 --- a/sci-libs/modglue/files/modglue-1.19-ldflags.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- src/Makefile.in.orig 2013-09-04 14:20:05.437329795 +1200 -+++ src/Makefile.in 2013-09-04 14:25:11.533806416 +1200 -@@ -21,9 +21,9 @@ - LTRELEASE = `echo ${RELEASE} | sed -e "s/\./:/g"` - - CPHASE = ${LIBTOOL} --tag=CXX --mode=compile @CXX@ -c @CFLAGS@ --LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} -rpath @prefix@@libdir@ @LIBS@ -+LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} @LDFLAGS@ -rpath @libdir@ @LIBS@ - #LPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -version-info ${LTRELEASE} @LIBS@ --MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ -+MPHASE = ${LIBTOOL} --tag=CXX --mode=link @CXX@ @LDFLAGS@ - IPHASE = ${LIBTOOL} --mode=install @INSTALL@ - FPHASE = ${LIBTOOL} --mode=finish @prefix@/@libdir@ - diff --git a/sci-libs/modglue/files/modglue-1.19-parallelmake.patch b/sci-libs/modglue/files/modglue-1.19-parallelmake.patch deleted file mode 100644 index b3dc35e7b..000000000 --- a/sci-libs/modglue/files/modglue-1.19-parallelmake.patch +++ /dev/null @@ -1,53 +0,0 @@ ---- Makefile.in.orig 2013-09-04 14:12:33.436620240 +1200 -+++ Makefile.in 2013-09-04 14:13:31.051711085 +1200 -@@ -8,7 +8,7 @@ - - library: - echo @libdir@ -- ( cd src && $(MAKE) ); -+ ( cd src && $(MAKE) library tools ); - - static: - ( cd src && $(MAKE) static ); ---- src/Makefile.in.orig 2013-09-04 14:13:46.820735926 +1200 -+++ src/Makefile.in 2013-09-04 14:15:46.020923434 +1200 -@@ -56,21 +56,21 @@ - - #------- Tests ---------------------------------------- - --test_child_process: test_child_process.o -+test_child_process: library test_child_process.o - ${MPHASE} -o test_child_process $< libmodglue.la - --test_ext_process: test_ext_process.o -+test_ext_process: library test_ext_process.o - ${MPHASE} -o test_ext_process $< libmodglue.la - --test_pipe: test_pipe.o -+test_pipe: library test_pipe.o - ${MPHASE} -o test_pipe $< libmodglue.la - --test_writes: test_writes.o -+test_writes: library test_writes.o - ${MPHASE} -o test_writes $< libmodglue.la - - #------- Tools ---------------------------------------- - --prompt: prompt.o -+prompt: library prompt.o - ${MPHASE} -o prompt prompt.o `pkg-config sigc++-2.0 --libs` libmodglue.la - # chrpath -d .libs/prompt - -@@ -85,10 +85,10 @@ - endif - - --ptywrap: ptywrap.o -+ptywrap: library ptywrap.o - ${MPHASE} -o ptywrap ptywrap.o @LINK_UTIL@ - --ptywrap_static: ptywrap.o -+ptywrap_static: library ptywrap.o - ${CPHASE} ${TIMESTAMP} -o ptywrap.o \ - -I@top_srcdir@/include -DSTATICBUILD ptywrap.cc - ifeq ($(strip $(MACTEST)),) diff --git a/sci-libs/modglue/modglue-1.19.ebuild b/sci-libs/modglue/modglue-1.19.ebuild index ca843118c..022049ce8 100644 --- a/sci-libs/modglue/modglue-1.19.ebuild +++ b/sci-libs/modglue/modglue-1.19.ebuild @@ -24,13 +24,8 @@ DEPEND="${RDEPEND} AUTOTOOLS_IN_SOURCE_BUILD=1 PATCHES=( - # Respect LDFLAGS (and a last bit of 64bit problem) - "${FILESDIR}"/${PN}-1.19-ldflags.patch - # fix parallel make. test are made at the same time as the library?? - "${FILESDIR}"/${PN}-1.19-parallelmake.patch - # take care of the lib/lib64 problem. Without this modglue installs - # stuff in /usr/usr/lib64 on 64bits systems. - "${FILESDIR}"/${PN}-1.16-lib64.patch + # consolidated (src/)Makefile.in patch + "${FILESDIR}"/${PN}-1.19-Makefiles.patch ) src_install() { diff --git a/sci-libs/scikits_image/ChangeLog b/sci-libs/scikits_image/ChangeLog index 2b3abdf68..116468d3f 100644 --- a/sci-libs/scikits_image/ChangeLog +++ b/sci-libs/scikits_image/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 20 Sep 2013; Justin Lecher <jlec@gentoo.org> scikits_image-9999.ebuild: + Merge tree changes + + 18 Sep 2013; Justin Lecher <jlec@gentoo.org> scikits_image-9999.ebuild, + metadata.xml: + Drop KEYWORDS from live ebuild + 17 Sep 2013; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml, scikits_image-9999.ebuild: sci-libs/scikits_image: Fix source directory, update dependencies, cleanup diff --git a/sci-libs/scikits_image/metadata.xml b/sci-libs/scikits_image/metadata.xml index 51476ec31..4e57c7f06 100644 --- a/sci-libs/scikits_image/metadata.xml +++ b/sci-libs/scikits_image/metadata.xml @@ -1,17 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> This SciKit (toolkit for SciPy) includes useful image processing algorithms for use with Python and NumPy. While SciPy’s ndimage provides low-level manipulation, scikits.image centres around algorithms and applications. </longdescription> -<use> - <flag name="freeimage">Enable support for image i/o via <pkg>media-libs/freeimage</pkg></flag> -</use> -<upstream> - <remote-id type="pypi">scikit-image</remote-id> -</upstream> + <use> + <flag name="freeimage">Enable support for image i/o via <pkg>media-libs/freeimage</pkg></flag> + </use> + <upstream> + <remote-id type="pypi">scikit-image</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/scikits_image/scikits_image-9999.ebuild b/sci-libs/scikits_image/scikits_image-9999.ebuild index bcb232c18..ebedf7b5d 100644 --- a/sci-libs/scikits_image/scikits_image-9999.ebuild +++ b/sci-libs/scikits_image/scikits_image-9999.ebuild @@ -16,7 +16,7 @@ EGIT_REPO_URI="https://github.com/scikit-image/scikit-image.git" LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +KEYWORDS="" IUSE="doc freeimage gtk qt4 test" RDEPEND=" @@ -40,8 +40,8 @@ python_test() { # distutils_install_for_testing not working here esetup.py \ install --root="${T}/test-${EPYTHON}" \ - --no-compile || die "install test failed" + --no-compile cd "${T}/test-${EPYTHON}/$(python_get_sitedir)" || die - echo "backend: Agg" > matplotlibrc + echo "backend: Agg" > matplotlibrc || die MPLCONFIGDIR=. nosetests -v skimage || die } diff --git a/sci-libs/wannier90/ChangeLog b/sci-libs/wannier90/ChangeLog index bb0da8817..ff8ee508f 100644 --- a/sci-libs/wannier90/ChangeLog +++ b/sci-libs/wannier90/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*wannier90-1.2-r2 (19 Sep 2013) + + 19 Sep 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + -wannier90-1.2-r1.ebuild, +wannier90-1.2-r2.ebuild: + Avoid sandbox violation when generating TeX fonts. + *wannier90-1.2-r1 (17 Jun 2013) 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-libs/wannier90/wannier90-1.2-r1.ebuild b/sci-libs/wannier90/wannier90-1.2-r2.ebuild index 252792245..481ce2b9a 100644 --- a/sci-libs/wannier90/wannier90-1.2-r1.ebuild +++ b/sci-libs/wannier90/wannier90-1.2-r2.ebuild @@ -48,7 +48,10 @@ src_configure() { src_compile() { emake -j1 wannier emake -j1 lib - use doc & emake -j1 doc + if use doc; then + VARTEXFONTS="${T}/fonts" + emake -j1 doc + fi } src_test() { |