From 7942c05fe297d82b7f4a1e81282aaa9b3bfb406a Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Thu, 30 Aug 2018 22:25:26 -0500 Subject: sci-mathematics/petsc: remove obsolete patches Package-Manager: Portage-2.3.48, Repoman-2.3.10 --- sci-mathematics/petsc/Manifest | 1 - .../petsc/files/petsc-3.5.3-disable-rpath.patch | 18 -- .../petsc/files/petsc-3.6.0-disable-rpath.patch | 17 -- .../files/petsc-3.6.0-fix_sandbox_violation.patch | 15 -- .../files/petsc-3.7.0-fix_sandbox_violation.patch | 17 -- sci-mathematics/petsc/petsc-3.7.7-r1.ebuild | 205 --------------------- 6 files changed, 273 deletions(-) delete mode 100644 sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch delete mode 100644 sci-mathematics/petsc/files/petsc-3.6.0-disable-rpath.patch delete mode 100644 sci-mathematics/petsc/files/petsc-3.6.0-fix_sandbox_violation.patch delete mode 100644 sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch delete mode 100644 sci-mathematics/petsc/petsc-3.7.7-r1.ebuild diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest index 35c4c980e..dd068b468 100644 --- a/sci-mathematics/petsc/Manifest +++ b/sci-mathematics/petsc/Manifest @@ -1,3 +1,2 @@ -DIST petsc-3.7.7.tar.gz 23200238 BLAKE2B 5fdee68949356da562cae14dfc8bb74f17ef8e07b8c69f495f212c2cd041b4f54597a3a53b3f0b3cf2f8484bc7f6f1b7db17b04328acb4b184519ff1a3bdc4a4 SHA512 408b176536c66b24ceebcc09ba94682d776b157a3eb841fe976b576fd4dc6073e65e76814f95d40a48f8c49dce3f4132dde0249ace64335ad37d2b347f0ed46d DIST petsc-3.8.4.tar.gz 27946435 BLAKE2B c4d71439695855bce0b6bd46ad434142adc9fd7a0d0b899fa5f02b9fefd65926470db02dfe250376416000031b54c230d338d3085472bad3d61a61b9f30f0713 SHA512 c186e143619c12d2175d01046c26221c462091706af0b68515ba1d2c93f97738ec375df7aa0551c5a14c240e80ca744f9d796778f4937a8c8021d64abe1f3b2c DIST petsc-3.9.2.tar.gz 29350029 BLAKE2B d8f8020f1e86633c82d71ca532c4a259930027be15e4ce9bb158fb3733ad2c6e01e355076661a3ebf37a81ccd3602687f6dfafa60792de2a9a7345863f658923 SHA512 d45901b4498eccd442773a3e4881e256efa46bf7126bd2f824e1a10dc62138a7c3821d648a6e63770fd10e5756fbe64af3cdbac5ba8301e7880fa72361301fc5 diff --git a/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch deleted file mode 100644 index 7fe3760c9..000000000 --- a/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py -index 8e0d2ee..ce53ad0 100644 ---- a/config/BuildSystem/config/setCompilers.py -+++ b/config/BuildSystem/config/setCompilers.py -@@ -1326,12 +1326,7 @@ class Configure(config.base.Configure): - for language in languages: - flag = '-L' - self.pushLanguage(language) -- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options. -- if not Configure.isDarwin(): -- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,'] -- else: -- testFlags = [] -- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not. -+ testFlags = [] - if self.isSun(self.framework.getCompiler()): - testFlags.insert(0,'-R') - for testFlag in testFlags: diff --git a/sci-mathematics/petsc/files/petsc-3.6.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.6.0-disable-rpath.patch deleted file mode 100644 index 88a7db565..000000000 --- a/sci-mathematics/petsc/files/petsc-3.6.0-disable-rpath.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py ---- a/config/BuildSystem/config/setCompilers.py -+++ b/config/BuildSystem/config/setCompilers.py -@@ -1326,12 +1326,7 @@ class Configure(config.base.Configure): - for language in languages: - flag = '-L' - self.pushLanguage(language) -- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options. -- if not Configure.isDarwin(): -- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,'] -- else: -- testFlags = ['-Wl,-rpath,'] -- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not. -+ testFlags = [] - if self.isSun(self.framework.getCompiler()): - testFlags.insert(0,'-R') - for testFlag in testFlags: diff --git a/sci-mathematics/petsc/files/petsc-3.6.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.6.0-fix_sandbox_violation.patch deleted file mode 100644 index 7510631a1..000000000 --- a/sci-mathematics/petsc/files/petsc-3.6.0-fix_sandbox_violation.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- config/PETSc/options/installDir.py.orig 2015-06-23 18:11:25.054911894 +0200 -+++ config/PETSc/options/installDir.py 2015-06-23 18:11:44.100289841 +0200 -@@ -38,12 +38,6 @@ - self.installSudoMessage = '' - if self.framework.argDB['prefix']: - self.dir = self.framework.argDB['prefix'] -- try: -- os.makedirs(os.path.join(self.dir,'PETScTestDirectory')) -- os.rmdir(os.path.join(self.dir,'PETScTestDirectory')) -- except: -- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs' -- self.installSudo = 'sudo ' - else: - self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) - self.confDir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch deleted file mode 100644 index 191ca18c4..000000000 --- a/sci-mathematics/petsc/files/petsc-3.7.0-fix_sandbox_violation.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py -index 0e2567c..bf782b5 100644 ---- a/config/PETSc/options/installDir.py -+++ b/config/PETSc/options/installDir.py -@@ -38,12 +38,6 @@ class Configure(config.base.Configure): - self.installSudoMessage = '' - if self.framework.argDB['prefix']: - self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix'])) -- try: -- os.makedirs(os.path.join(self.dir,'PETScTestDirectory')) -- os.rmdir(os.path.join(self.dir,'PETScTestDirectory')) -- except: -- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs' -- self.installSudo = 'sudo ' - else: - self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) - self.confDir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) diff --git a/sci-mathematics/petsc/petsc-3.7.7-r1.ebuild b/sci-mathematics/petsc/petsc-3.7.7-r1.ebuild deleted file mode 100644 index ddd6202e0..000000000 --- a/sci-mathematics/petsc/petsc-3.7.7-r1.ebuild +++ /dev/null @@ -1,205 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 ) - -inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator - -MY_P="${PN}-$(replace_version_separator _ -)" - -DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" -HOMEPAGE="http://www.mcs.anl.gov/petsc/" -SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="afterimage boost complex-scalars cxx debug doc fftw - fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X" - -# hypre and superlu curretly exclude each other due to missing linking to hypre -# if both are enabled -REQUIRED_USE=" - afterimage? ( X ) - complex-scalars? ( !hypre !superlu ) - hdf5? ( mpi ) - hypre? ( cxx mpi !superlu ) - mumps? ( mpi scotch ) - scotch? ( mpi ) - superlu? ( !hypre ) -" - -RDEPEND=" - virtual/blas - virtual/lapack - afterimage? ( media-libs/libafterimage ) - boost? ( dev-libs/boost ) - fftw? ( sci-libs/fftw:3.0[mpi?] ) - hdf5? ( sci-libs/hdf5[mpi?] ) - hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) - metis? ( >=sci-libs/parmetis-4 ) - mpi? ( virtual/mpi[cxx?,fortran?] ) - mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) - scotch? ( sci-libs/scotch[mpi?] ) - sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) - superlu? ( >=sci-libs/superlu-5 ) - X? ( x11-libs/libX11 ) -" - -DEPEND="${RDEPEND} - ${PYTHON_DEPS} - virtual/pkgconfig - dev-util/cmake -" - -# -# PETSc does not want its Makefiles to be invoked with anything higher than -# -j1. The underlying build system does automatically invoke a parallel -# build. This might not be what you want, but *hey* not your choice. -# -# V=1 enables verbose output with full compiler and linker invocation -# -MAKEOPTS="${MAKEOPTS} -j1 V=1" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \ - "${FILESDIR}"/${PN}-3.7.0-fix_sandbox_violation.patch -) - -src_prepare() { - default - - sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die -} - -# petsc uses --with-blah=1 and --with-blah=0 to en/disable options -petsc_enable() { - use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" -} -# add external library: -# petsc_with use_flag libname libdir -# petsc_with use_flag libname include linking_libs -petsc_with() { - local myuse p=${2:-${1}} - if use ${1}; then - myuse="--with-${p}=1" - if [[ $# -ge 4 ]]; then - myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" - shift 3 - myuse="${myuse} --with-${p}-lib=$@" - else - myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}" - fi - else - myuse="--with-${p}=0" - fi - echo ${myuse} -} - -# select between configure options depending on use flag -petsc_select() { - use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" -} - -src_configure() { - # bug 548498 - # PETSc runs mpi processes during configure that result in a sandbox - # violation by trying to open /proc/mtrr rw. This is not easy to - # mitigate because it happens in libpciaccess.so called by libhwloc.so, - # which is used by libmpi.so. - addpredict /proc/mtrr - # if mpi is built with knem support it needs /dev/knem too - addpredict /dev/knem - - # configureMPITypes with openmpi-2* insists on accessing the scaling - # governor rw. - addpredict /sys/devices/system/cpu/ - - local mylang - local myopt - - use cxx && mylang="cxx" || mylang="c" - use debug && myopt="debug" || myopt="opt" - - # environmental variables expected by petsc during build - - export PETSC_DIR="${S}" - export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" - - if use debug; then - strip-flags - filter-flags -O* - fi - - # C Support on CXX builds is enabled if possible i.e. when not using - # complex scalars (no complex type for both available at the same time) - - econf \ - scrollOutput=1 \ - FFLAGS="${FFLAGS} -fPIC" \ - CFLAGS="${CFLAGS} -fPIC" \ - CXXFLAGS="${CXXFLAGS} -fPIC" \ - LDFLAGS="${LDFLAGS}" \ - --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \ - --with-shared-libraries \ - --with-single-library \ - --with-clanguage=${mylang} \ - $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ - --with-petsc-arch=${PETSC_ARCH} \ - --with-precision=double \ - --with-gnu-compilers \ - --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \ - $(petsc_enable debug debugging) \ - $(petsc_enable mpi) \ - $(petsc_select mpi cc mpicc $(tc-getCC)) \ - $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ - $(petsc_enable fortran) \ - $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ - $(petsc_enable mpi mpi-compilers) \ - $(petsc_select complex-scalars scalar-type complex real) \ - --with-windows-graphics=0 \ - --with-matlab=0 \ - --with-cmake=cmake \ - $(petsc_enable threads pthread) \ - $(petsc_with afterimage afterimage \ - /usr/include/libAfterImage -lAfterImage) \ - $(petsc_with hdf5) \ - $(petsc_with hypre hypre \ - /usr/include/hypre -lHYPRE) \ - $(petsc_with sparse suitesparse) \ - $(petsc_with superlu superlu \ - /usr/include/superlu -lsuperlu) \ - $(petsc_with X x) \ - $(petsc_with X x11) \ - $(petsc_with scotch ptscotch \ - /usr/include/scotch \ - [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ - $(petsc_with mumps scalapack \ - /usr/include/scalapack -lscalapack) \ - $(petsc_with mumps mumps \ - /usr/include \ - [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ - --with-imagemagick=0 \ - --with-python=0 \ - $(petsc_with boost) \ - $(petsc_with fftw) -} - -src_install() { - emake DESTDIR="${D}/usr/$(get_libdir)/petsc" install - - # add PETSC_DIR to environmental variables - cat >> 99petsc <<- EOF - PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc - EOF - doenvd 99petsc - - if use doc ; then - dodoc docs/developers.pdf docs/manual.pdf - dohtml -r docs/*.html docs/changes docs/manualpages - fi -} -- cgit v1.2.3-18-g5258