diff --git a/math/deal.ii/Makefile b/math/deal.ii/Makefile index 1cb851e07328..deec17783b2d 100644 --- a/math/deal.ii/Makefile +++ b/math/deal.ii/Makefile @@ -1,96 +1,96 @@ PORTNAME= deal.II DISTVERSIONPREFIX= v DISTVERSION= 9.3.1 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Finite element Differential Equations Analysis Library (DEAL) LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE.md BROKEN_FreeBSD_14= clang crashes: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=257876 BUILD_DEPENDS= ${LOCALBASE}/include/boost/config.hpp:devel/boost-libs LIB_DEPENDS= libboost_serialization.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ libmetis.so:math/metis USES= blaslapack cmake compiler:c++17-lang localbase:ldflags USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= ${PORTNAME:tl:S/.//} GH_PROJECT= ${PORTNAME:tl:S/.//} CMAKE_OFF= DEAL_II_ALLOW_BUNDLED DEAL_II_COMPONENT_EXAMPLES \ DEAL_II_WITH_P4EST DEAL_II_WITH_TRILINOS DEAL_II_WITH_UMFPACK \ DEAL_II_WITH_NANOFLANN DEAL_II_WITH_MUPARSER DEAL_II_WITH_ASSIMP \ DEAL_II_WITH_HDF5 CMAKE_ON= DEAL_II_FORCE_BUNDLED_TBB # instead of LIB_DEPENDS+=libtbb.so:devel/onetbb, pending https://github.com/dealii/dealii/issues/11561 OPTIONS_DEFINE= ADOLC ARPACK GSL LAPACK MPI NETCDF OPENCASCADE PETSC SCALAPACK SUNDIALS OPTIONS_DEFAULT= GSL LAPACK # SUNDIALS ADOLC_DESC= Compile with ADOL-C ADOLC_CMAKE_BOOL= DEAL_II_WITH_ADOLC ADOLC_LIB_DEPENDS= libadolc.so:math/adol-c ADOLC_BROKEN= requires the development version: see https://github.com/dealii/dealii/issues/7293 ARPACK_DESC= Compile with Arpack and PArpack (only with MPI, LAPACK) ARPACK_CMAKE_BOOL= DEAL_II_WITH_ARPACK ARPACK_CMAKE_ON= -DARPACK_LINKER_FLAGS:STRING="${LDFLAGS}" ARPACK_BUILD_DEPENDS= arpack-ng>0:math/arpack-ng ARPACK_RUN_DEPENDS= arpack-ng>0:math/arpack-ng # itself doesn't link to arpack, but makes depending project link to it ARPACK_IMPLIES= LAPACK GSL_DESC= Compile with gsl GSL_CMAKE_BOOL= DEAL_II_WITH_GSL GSL_LIB_DEPENDS= libgsl.so:math/gsl LAPACK_DESC= Compile with LAPACK for matrix operations LAPACK_USES= fortran LAPACK_CMAKE_BOOL= DEAL_II_WITH_LAPACK LAPACK_CMAKE_ON= -DLAPACK_LINKER_FLAGS:STRING="${LDFLAGS}" LAPACK_LIB_DEPENDS= libopenblas.so:math/openblas MPI_DESC= MPI support (math/sundials must be compiled with MPI) MPI_USES= fortran MPI_CMAKE_BOOL= DEAL_II_WITH_MPI MPI_CMAKE_ON= -DMPI_LINKER_FLAGS:STRING="${LDFLAGS}" MPI_LIB_DEPENDS= libboost_iostreams.so:devel/boost-libs \ libmpich.so:net/mpich NETCDF_DESC= Compile with Netcdf (only with MPI) NETCDF_CMAKE_BOOL= DEAL_II_WITH_NETCDF NETCDF_CMAKE_ON= -DNETCDF_INCLUDE_DIR:STRING=${LOCALBASE}/include -DNETCDF_CPLUSPLUS_LIBRARY:STRING=${LOCALBASE}/lib/libnetcdf_c++4.so NETCDF_BROKEN= see https://github.com/dealii/dealii/issues/7263 OPENCASCADE_DESC= Compile with OpenCascade OPENCASCADE_CMAKE_BOOL= DEAL_II_WITH_OPENCASCADE OPENCASCADE_CMAKE_ON= -DOPENCASCADE_INCLUDE_DIR:STRING=${LOCALBASE}/include/OpenCASCADE OPENCASCADE_LIB_DEPENDS= libTKernel.so:cad/opencascade PETSC_DESC= Compile with Petsc (only with MPI) PETSC_CMAKE_BOOL= DEAL_II_WITH_PETSC PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc PETSC_BROKEN= see https://github.com/dealii/dealii/issues/7260 SCALAPACK_DESC= Compile with ScaLAPACK (only with MPI) SCALAPACK_CMAKE_BOOL= DEAL_II_WITH_SCALAPACK SCALAPACK_IMPLIES= MPI LAPACK SCALAPACK_LIB_DEPENDS= libscalapack.so:math/scalapack SUNDIALS_DESC= Compile with SUNDIALS SUNDIALS_CMAKE_BOOL= DEAL_II_WITH_SUNDIALS SUNDIALS_LIB_DEPENDS= libsundials_arkode.so:math/sundials SUNDIALS_BROKEN= Build fails with: Required variable "SUNDIALS_LIB_PAR" set to NOTFOUND post-patch: # unbundle boost @${RM} -r ${WRKSRC}/dealii/bundled/boost-* post-stage: @${RM} ${STAGEDIR}${PREFIX}/*.log .include diff --git a/math/mcsim/Makefile b/math/mcsim/Makefile index 094795dc76dd..117486f6ce4f 100644 --- a/math/mcsim/Makefile +++ b/math/mcsim/Makefile @@ -1,45 +1,46 @@ # Created by: Alessando Sagratini PORTNAME= mcsim PORTVERSION= 6.2.0 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= GNU MAINTAINER= ale_sagra@hotmail.com COMMENT= Monte Carlo stochastic simulations and Bayesian inference LICENSE= GPLv3+ BUILD_DEPENDS= indexinfo>=0.3.0:print/indexinfo USES= libtool shebangfix USE_LDCONFIG= yes INFO= mcsim SHEBANG_FILES= sim/makemcsim.in sim/makemcsims.in sim/makemcsimd.in sim/makemcsimp.in INSTALL_TARGET= install-strip GNU_CONFIGURE= yes OPTIONS_SUB= yes CONFIGURE_ARGS= --prefix=${PREFIX} OPTIONS_DEFINE= GSL SUNDIALS GSL_DESC= GNU Scientific Library support (recommended) SUNDIALS_DESC= Sundial's Cvodes integrator OPTIONS_DEFAULT=GSL .include .if ${PORT_OPTIONS:MSUNDIALS} BUILD_DEPENDS+= sundials>=3.0.0:math/sundials .endif .if ${PORT_OPTIONS:MGSL} BUILD_DEPENDS+= gsl>=2.5:math/gsl .endif .include diff --git a/math/octave/Makefile b/math/octave/Makefile index 7d7f49233761..da7c7d7f65a9 100644 --- a/math/octave/Makefile +++ b/math/octave/Makefile @@ -1,138 +1,138 @@ # Created by: chuckr@FreeBSD.org PORTNAME= octave PORTVERSION= ${OCTAVE_VERSION} -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math MASTER_SITES= GNU MAINTAINER= stephen@FreeBSD.org COMMENT= High-level interactive language for numerical computations LICENSE= GPLv3 BUILD_DEPENDS= gnuplot:math/gnuplot \ ${LOCALBASE}/bin/gperf:devel/gperf \ gsed:textproc/gsed \ ${LOCALBASE}/bin/makeinfo:print/texinfo RUN_DEPENDS= gnuplot:math/gnuplot \ gsed:textproc/gsed \ ${LOCALBASE}/bin/makeinfo:print/texinfo LIB_DEPENDS= libGraphicsMagick.so:graphics/GraphicsMagick \ libarpack.so:math/arpack-ng \ libcurl.so:ftp/curl \ libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float \ libfltk.so:x11-toolkits/fltk \ libftgl.so:graphics/ftgl \ libhdf5.so:science/hdf5 \ libpcre.so:devel/pcre \ libqhull.so.7:math/qhull \ libqrupdate.so:math/qrupdate \ libamd.so:math/suitesparse-amd \ libcamd.so:math/suitesparse-camd \ libccolamd.so:math/suitesparse-ccolamd \ libcholmod.so:math/suitesparse-cholmod \ libcolamd.so:math/suitesparse-colamd \ libsuitesparseconfig.so:math/suitesparse-config \ libcxsparse.so:math/suitesparse-cxsparse \ libklu.so:math/suitesparse-klu \ libumfpack.so:math/suitesparse-umfpack \ libglpk.so:math/glpk \ libgl2ps.so:print/gl2ps \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libdrm.so:graphics/libdrm \ libOSMesa.so:graphics/libosmesa \ libsundials_arkode.so:math/sundials \ libportaudio.so:audio/portaudio # libsndfile.so:audio/libsndfile # Commented out until this port no longer has vulnerabilities. USES= charsetfix fortran gmake libtool perl5 pkgconfig readline \ tar:xz compiler:c++14-lang \ desktop-file-utils gl iconv ncurses xorg USE_LDCONFIG= ${PREFIX}/lib/${PORTNAME}/${PORTVERSION} USE_PERL5= build GNU_CONFIGURE= yes USE_QT= core gui help network opengl \ qmake_build buildtools_build linguist_build \ printsupport sql widgets \ xml USE_XORG= x11 xext xfixes xft \ xcursor xinerama xrender USE_GL= gl glu OCTAVE_VERSION= ${PORTVERSION} GNU_HOST= ${ARCH}-portbld-freebsd${OSREL} PLIST_SUB= OCTAVE_VERSION=${OCTAVE_VERSION} GNU_HOST=${GNU_HOST} CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib -L${LOCALBASE}/lib/qt5 CONFIGURE_ENV= GPERF="${LOCALBASE}/bin/gperf" \ JAVA_HOME=${JAVA_HOME} \ MAKEINFO=${LOCALBASE}/bin/makeinfo \ MKINFO=${LOCALBASE}/bin/makeinfo \ MOC_QTVER=${MOC} \ UIC_QTVER=${UIC} \ RCC_QTVER=${RCC} \ LRELEASE_QTVER=${LRELEASE} \ QCOLLECTIONGENERATOR_QTVER=${QCOLLECTIONGENERATOR} \ QHELPGENERATOR_QTVER=${QHELPGENERATOR} \ ac_cv_type_max_align_t=yes \ ac_cv_path_SED=${LOCALBASE}/bin/gsed CONFIGURE_ARGS= --host=${GNU_HOST} \ --with-blas="-L${LOCALBASE}/lib ${BLASLIB}" \ --with-lapack="${LAPACKLIB}" \ --enable-shared \ --disable-jit \ --disable-openmp \ --with-osmesa INFO= octave liboctave INSTALL_TARGET= install-strip OPTIONS_DEFINE= DOCS JAVA QT5 OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= OPENBLAS NETLIB ATLAS OPTIONS_DEFAULT= JAVA OPENBLAS QT5 OPTIONS_SUB= yes DOCS_CONFIGURE_ENABLE= docs JAVA_CONFIGURE_ENABLE= java QT5_CONFIGURE_WITH= qt=5 qscintilla QT5_LIB_DEPENDS= libqscintilla2_qt5.so:devel/qscintilla2-qt5 DOCS_USE= TEX=dvipsk:build,formats:build JAVA_USE= JAVA=yes QT5_USES= qt:5 OPENBLAS_USES= blaslapack:openblas NETLIB_USES= blaslapack:netlib ATLAS_USES= blaslapack:atlas post-patch: ${REINPLACE_CMD} 's+"makeinfo"+"${LOCALBASE}/bin/makeinfo"+' ${WRKSRC}/libinterp/corefcn/help.cc ${REINPLACE_CMD} 's/"-qt=$$qt_version"/"-qt=qt$$qt_version"/' ${WRKSRC}/configure post-install: (cd ${STAGEDIR}${DATADIR} && ${LN} -s ${PORTVERSION}/imagelib .) post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} .for file in liboctave/liboctave.ps \ refcard/refcard-a4.ps refcard/refcard-legal.ps \ refcard/refcard-letter.ps interpreter/octave.ps ${INSTALL_DATA} ${WRKSRC}/doc/${file} ${STAGEDIR}${DOCSDIR} .endfor @${MKDIR} ${STAGEDIR}${PREFIX}/${INFO_PATH} .for file in interpreter/octave.info liboctave/liboctave.info ${INSTALL_DATA} ${WRKSRC}/doc/${file} ${STAGEDIR}${PREFIX}/${INFO_PATH} .endfor check regression-test: build @(cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} check) .include "Makefile.version" .include diff --git a/math/sundials/Makefile b/math/sundials/Makefile index 65b66fabcd47..94f9d2135dc4 100644 --- a/math/sundials/Makefile +++ b/math/sundials/Makefile @@ -1,69 +1,70 @@ PORTNAME= sundials -DISTVERSION= 3.1.2 -PORTREVISION= 11 +DISTVERSION= 5.7.0 CATEGORIES= math -MASTER_SITES= https://computation.llnl.gov/projects/sundials/download/ +MASTER_SITES= https://github.com/LLNL/sundials/releases/download/v${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE -USES= cmake:noninja python:build # ninja doesn't support fortran +USES= cmake:noninja fortran localbase:ldflags python:build # ninja doesn't support fortran USE_LDCONFIG= yes -CMAKE_ARGS= -DPTHREAD_ENABLE:BOOL=ON \ +CMAKE_ARGS= -DENABLE_PTHREAD:BOOL=ON \ -DBUILD_STATIC_LIBS:BOOL=OFF -PLIST_SUB= SHL3=${DISTVERSION} SHL1=${DISTVERSION:R:R} SHLX3=1.1.2 SHLX1=1 +FCFLAGS:= ${FFLAGS} # project checks that these flags are equal + +TEST_TARGET= test OPTIONS_DEFINE= BLAS EXAMPLES LAPACK MPI # OPENMP detection is broken in cmake: https://gitlab.kitware.com/cmake/cmake/issues/17474 -OPTIONS_DEFAULT= LAPACK +#OPTIONS_DEFAULT= LAPACK # LAPACK is broken OPTIONS_GROUP= VECTORS OPTIONS_GROUP_VECTORS= HYPRE PETSC VECTORS_DESC= Alternative vector libraries -BLAS_DESC= Enable BLAS support -HYPRE_DESC= HYPRE vectors support (also enables MPI) -LAPACK_DESC= Use Lapack linear algebra (sets SUNDIALS_INDEX_TYPE=int32) -PETSC_DESC= PETSc vectors support (also enables MPI) OPTIONS_SUB= yes +BLAS_DESC= Enable BLAS support BLAS_CMAKE_BOOL= BLAS_ENABLE -BLAS_USES= blaslapack:openblas fortran +BLAS_USES= blaslapack:openblas BLAS_CMAKE_ON= -DFREEBSD_GCC_DIR:STRING=${LOCALBASE}/lib/gcc${GCC_DEFAULT:S/.//} # assumes that fortran:gcc is used EXAMPLES_CMAKE_BOOL= EXAMPLES_ENABLE_C EXAMPLES_ENABLE_CXX EXAMPLES_ENABLE_F77 EXAMPLES_ENABLE_F90 EXAMPLES_CMAKE_ON= -DEXAMPLES_INSTALL_PATH=${EXAMPLESDIR} -HYPRE_CMAKE_BOOL= HYPRE_ENABLE +HYPRE_DESC= HYPRE vectors support (also enables MPI) +HYPRE_CMAKE_BOOL= ENABLE_HYPRE HYPRE_CMAKE_ON= -DHYPRE_INCLUDE_DIR=${LOCALBASE}/include \ -DHYPRE_LIBRARY_DIR=${LOCALBASE}/lib -HYPRE_LIB_DEPENDS= libHYPRE.so:science/hypre +HYPRE_LIB_DEPENDS= libHYPRE.so:science/hypre # maybe is broken due to https://github.com/hypre-space/hypre/issues/464 HYPRE_IMPLIES= MPI HYPRE_PREVENTS= LAPACK # error: Incompatible sunindextype for LAPACK; disable LAPACK and rebuild -LAPACK_USES= blaslapack:openblas fortran -LAPACK_CMAKE_BOOL= LAPACK_ENABLE -LAPACK_CMAKE_ON= -DSUNDIALS_INDEX_TYPE:STRING=int32_t \ +LAPACK_DESC= Use Lapack linear algebra (sets SUNDIALS_INDEX_TYPE=int32) +LAPACK_USES= blaslapack:openblas +LAPACK_CMAKE_BOOL= ENABLE_LAPACK +LAPACK_CMAKE_ON= -DSUNDIALS_INDEX_TYPE:STRING=int64_t \ -DFREEBSD_GCC_DIR:STRING=${LOCALBASE}/lib/gcc${GCC_DEFAULT:S/.//} # assumes that fortran:gcc is used +LAPACK_BROKEN= Ignores LDFLAGS and fails to find lapack: https://github.com/LLNL/sundials/issues/74 MPI_CMAKE_ON= -DMPI_ENABLE:BOOL=ON MPI_LIB_DEPENDS= libmpich.so:net/mpich -PETSC_CMAKE_BOOL= PETSC_ENABLE -PETSC_CMAKE_ON= -DPETSC_INCLUDE_DIR=${LOCALBASE}/include \ +PETSC_DESC= PETSc vectors support (also enables MPI) +PETSC_CMAKE_BOOL= ENABLE_PETSC +PETSC_CMAKE_ON= -DPETSC_DIR=${LOCALBASE} \ + -DPETSC_INCLUDE_DIR=${LOCALBASE}/include \ -DPETSC_LIBRARY_DIR=${LOCALBASE}/lib PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc PETSC_IMPLIES= MPI PETSC_PREVENTS= LAPACK # error: Incompatible sunindextype for LAPACK; disable LAPACK and rebuild +PERSC_BROKEN= ERROR: PETSc not functional due to index size mismatch: SUNDIALS_INDEX_SIZE=64, but PETSc was built with 32-bit indices PORTEXAMPLES= * -post-patch: - @${FIND} ${WRKSRC}/examples -name "*.c" -o -name "*.cpp" | ${XARGS} ${REINPLACE_CMD} -E 's/"(ESYM|FSYM)"/" \1 "/g' - post-install: @${RM} ${STAGEDIR}${PREFIX}/include/sundials/LICENSE .include diff --git a/math/sundials/distinfo b/math/sundials/distinfo index c64cf3e65774..a10e2e95c308 100644 --- a/math/sundials/distinfo +++ b/math/sundials/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1533629106 -SHA256 (sundials-3.1.2.tar.gz) = a8985bb1e851d90e24260450667b134bc13d71f5c6effc9e1d7183bd874fe116 -SIZE (sundials-3.1.2.tar.gz) = 18212893 +TIMESTAMP = 1630044758 +SHA256 (sundials-5.7.0.tar.gz) = 48da7baa8152ddb22aed1b02d82d1dbb4fbfea22acf67634011aa0303a100a43 +SIZE (sundials-5.7.0.tar.gz) = 22612286 diff --git a/math/sundials/files/patch-config_SundialsBlas.cmake b/math/sundials/files/patch-config_SundialsBlas.cmake deleted file mode 100644 index 74a9406d0ff4..000000000000 --- a/math/sundials/files/patch-config_SundialsBlas.cmake +++ /dev/null @@ -1,10 +0,0 @@ ---- config/SundialsBlas.cmake.orig 2017-11-07 23:47:45 UTC -+++ config/SundialsBlas.cmake -@@ -74,6 +74,7 @@ if(BLAS_LIBRARIES) - - # Attempt to link the "ltest" executable - try_compile(LTEST_OK ${BlasTest_DIR} ${BlasTest_DIR} -+ LINK_DIRECTORIES ${FREEBSD_GCC_DIR} - ltest OUTPUT_VARIABLE MY_OUTPUT) - - # To ensure we do not use stuff from the previous attempts, diff --git a/math/sundials/files/patch-config_SundialsFortran.cmake b/math/sundials/files/patch-config_SundialsFortran.cmake deleted file mode 100644 index 561332abb4ba..000000000000 --- a/math/sundials/files/patch-config_SundialsFortran.cmake +++ /dev/null @@ -1,15 +0,0 @@ ---- config/SundialsFortran.cmake.orig 2017-11-07 23:47:45 UTC -+++ config/SundialsFortran.cmake -@@ -51,9 +51,9 @@ if(CMAKE_Fortran_COMPILER) - (NOT "${ENV_FCFLAGS}" STREQUAL "") AND - ("${CMAKE_Fortran_FLAGS}" STREQUAL "")) - # check if environment variables are equal -- IF (NOT "${ENV_FFLAGS}" STREQUAL "${ENV_FCFLAGS}") -- PRINT_ERROR("FFLAGS='${ENV_FFLAGS}' and FCFLAGS='${ENV_FCFLAGS}' are both set but are not equal.") -- ENDIF() -+ #IF (NOT "${ENV_FFLAGS}" STREQUAL "${ENV_FCFLAGS}") -+ # PRINT_ERROR("FFLAGS='${ENV_FFLAGS}' and FCFLAGS='${ENV_FCFLAGS}' are both set but are not equal.") -+ #ENDIF() - ENDIF() - - # Enable the language for next steps diff --git a/math/sundials/files/patch-config_SundialsFortran90.cmake b/math/sundials/files/patch-config_SundialsFortran90.cmake deleted file mode 100644 index 081d9cbc4dc5..000000000000 --- a/math/sundials/files/patch-config_SundialsFortran90.cmake +++ /dev/null @@ -1,15 +0,0 @@ ---- config/SundialsFortran90.cmake.orig 2017-11-07 23:47:45 UTC -+++ config/SundialsFortran90.cmake -@@ -35,9 +35,9 @@ if(CMAKE_Fortran_COMPILER) - (NOT "${ENV_FCFLAGS}" STREQUAL "") AND - ("${CMAKE_Fortran_FLAGS}" STREQUAL "")) - # check if environment variables are equal -- IF (NOT "${ENV_FFLAGS}" STREQUAL "${ENV_FCFLAGS}") -- PRINT_ERROR("FFLAGS='${ENV_FFLAGS}' and FCFLAGS='${ENV_FCFLAGS}' are both set but are not equal.") -- ENDIF() -+ #IF (NOT "${ENV_FFLAGS}" STREQUAL "${ENV_FCFLAGS}") -+ # PRINT_ERROR("FFLAGS='${ENV_FFLAGS}' and FCFLAGS='${ENV_FCFLAGS}' are both set but are not equal.") -+ #ENDIF() - ENDIF() - - # Enable the language for next steps diff --git a/math/sundials/files/patch-config_SundialsLapack.cmake b/math/sundials/files/patch-config_SundialsLapack.cmake deleted file mode 100644 index 248f4d07f0cf..000000000000 --- a/math/sundials/files/patch-config_SundialsLapack.cmake +++ /dev/null @@ -1,10 +0,0 @@ ---- config/SundialsLapack.cmake.orig 2017-11-07 23:47:45 UTC -+++ config/SundialsLapack.cmake -@@ -75,6 +75,7 @@ if(LAPACK_LIBRARIES) - - # Attempt to link the "ltest" executable - try_compile(LTEST_OK ${LapackTest_DIR} ${LapackTest_DIR} -+ LINK_DIRECTORIES ${FREEBSD_GCC_DIR} - ltest OUTPUT_VARIABLE MY_OUTPUT) - - # To ensure we do not use stuff from the previous attempts, diff --git a/math/sundials/files/patch-config_SundialsSuperLUMT.cmake b/math/sundials/files/patch-config_SundialsSuperLUMT.cmake deleted file mode 100644 index 2b0a1670ab19..000000000000 --- a/math/sundials/files/patch-config_SundialsSuperLUMT.cmake +++ /dev/null @@ -1,11 +0,0 @@ ---- config/SundialsSuperLUMT.cmake.orig 2017-12-28 04:44:39 UTC -+++ config/SundialsSuperLUMT.cmake -@@ -61,7 +61,7 @@ if(SUPERLUMT_LIBRARY AND SUPERLUMT_LIBRA - "}\n") - - # Attempt to link the "ltest" executable -- try_compile(LTEST_OK ${SUPERLUMT_TEST_DIR} ${SUPERLUMT_TEST_DIR} ltest OUTPUT_VARIABLE MY_OUTPUT) -+ try_compile(LTEST_OK ${SUPERLUMT_TEST_DIR} ${SUPERLUMT_TEST_DIR} LINK_DIRECTORIES ${FREEBSD_GCC_DIR} ltest OUTPUT_VARIABLE MY_OUTPUT) - - # To ensure we do not use stuff from the previous attempts, - # we must remove the CMakeFiles directory. diff --git a/math/sundials/files/patch-src_arkode_CMakeLists.txt b/math/sundials/files/patch-src_arkode_CMakeLists.txt deleted file mode 100644 index 93a9caa23adf..000000000000 --- a/math/sundials/files/patch-src_arkode_CMakeLists.txt +++ /dev/null @@ -1,22 +0,0 @@ ---- src/arkode/CMakeLists.txt.orig 2017-11-07 23:47:45 UTC -+++ src/arkode/CMakeLists.txt -@@ -112,6 +112,19 @@ IF(BUILD_SHARED_LIBS) - TARGET_LINK_LIBRARIES(sundials_arkode_shared m) - ENDIF() - -+ -+ IF(UNIX) -+ TARGET_LINK_LIBRARIES(sundials_arkode_shared m) -+ ENDIF() -+ -+ IF(LAPACK_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_arkode_shared ${LAPACK_LIBRARIES}) -+ ENDIF() -+ -+ IF(KLU_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_arkode_shared ${KLU_LIBRARIES}) -+ ENDIF () -+ - # Set the library name and make sure it is not deleted - SET_TARGET_PROPERTIES(sundials_arkode_shared - PROPERTIES OUTPUT_NAME sundials_arkode CLEAN_DIRECT_OUTPUT 1) diff --git a/math/sundials/files/patch-src_cvode_CMakeLists.txt b/math/sundials/files/patch-src_cvode_CMakeLists.txt deleted file mode 100644 index 03b9411207cf..000000000000 --- a/math/sundials/files/patch-src_cvode_CMakeLists.txt +++ /dev/null @@ -1,21 +0,0 @@ ---- src/cvode/CMakeLists.txt.orig 2017-11-07 23:47:57 UTC -+++ src/cvode/CMakeLists.txt -@@ -114,6 +114,18 @@ IF(BUILD_SHARED_LIBS) - TARGET_LINK_LIBRARIES(sundials_cvode_shared m) - ENDIF() - -+ IF(UNIX) -+ TARGET_LINK_LIBRARIES(sundials_cvode_shared m) -+ ENDIF() -+ -+ IF(LAPACK_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_cvode_shared ${LAPACK_LIBRARIES}) -+ ENDIF() -+ -+ IF(KLU_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_cvode_shared ${KLU_LIBRARIES}) -+ ENDIF () -+ - # Set the library name and make sure it is not deleted - SET_TARGET_PROPERTIES(sundials_cvode_shared - PROPERTIES OUTPUT_NAME sundials_cvode CLEAN_DIRECT_OUTPUT 1) diff --git a/math/sundials/files/patch-src_cvodes_CMakeLists.txt b/math/sundials/files/patch-src_cvodes_CMakeLists.txt deleted file mode 100644 index 9cc862d4f65d..000000000000 --- a/math/sundials/files/patch-src_cvodes_CMakeLists.txt +++ /dev/null @@ -1,21 +0,0 @@ ---- src/cvodes/CMakeLists.txt.orig 2017-11-07 23:48:01 UTC -+++ src/cvodes/CMakeLists.txt -@@ -116,6 +116,18 @@ IF(BUILD_SHARED_LIBS) - TARGET_LINK_LIBRARIES(sundials_cvodes_shared m) - ENDIF() - -+ IF(UNIX) -+ TARGET_LINK_LIBRARIES(sundials_cvodes_shared m) -+ ENDIF() -+ -+ IF(LAPACK_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_cvodes_shared ${LAPACK_LIBRARIES}) -+ ENDIF() -+ -+ IF(KLU_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_cvodes_shared ${KLU_LIBRARIES}) -+ ENDIF() -+ - # Set the library name and make sure it is not deleted - SET_TARGET_PROPERTIES(sundials_cvodes_shared - PROPERTIES OUTPUT_NAME sundials_cvodes CLEAN_DIRECT_OUTPUT 1) diff --git a/math/sundials/files/patch-src_ida_CMakeLists.txt b/math/sundials/files/patch-src_ida_CMakeLists.txt deleted file mode 100644 index b44f0c2b63a6..000000000000 --- a/math/sundials/files/patch-src_ida_CMakeLists.txt +++ /dev/null @@ -1,21 +0,0 @@ ---- src/ida/CMakeLists.txt.orig 2017-11-07 23:48:06 UTC -+++ src/ida/CMakeLists.txt -@@ -117,6 +117,18 @@ IF(BUILD_SHARED_LIBS) - TARGET_LINK_LIBRARIES(sundials_ida_shared m) - ENDIF() - -+ IF(UNIX) -+ TARGET_LINK_LIBRARIES(sundials_ida_shared m) -+ ENDIF() -+ -+ IF(LAPACK_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_ida_shared ${LAPACK_LIBRARIES}) -+ ENDIF() -+ -+ IF(KLU_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_ida_shared ${KLU_LIBRARIES}) -+ ENDIF() -+ - # Set the library name and make sure it is not deleted - SET_TARGET_PROPERTIES(sundials_ida_shared - PROPERTIES OUTPUT_NAME sundials_ida CLEAN_DIRECT_OUTPUT 1) diff --git a/math/sundials/files/patch-src_idas_CMakeLists.txt b/math/sundials/files/patch-src_idas_CMakeLists.txt deleted file mode 100644 index 473abaef7f15..000000000000 --- a/math/sundials/files/patch-src_idas_CMakeLists.txt +++ /dev/null @@ -1,21 +0,0 @@ ---- src/idas/CMakeLists.txt.orig 2017-11-07 23:48:10 UTC -+++ src/idas/CMakeLists.txt -@@ -113,6 +113,18 @@ IF(BUILD_SHARED_LIBS) - TARGET_LINK_LIBRARIES(sundials_idas_shared m) - ENDIF() - -+ IF(UNIX) -+ TARGET_LINK_LIBRARIES(sundials_idas_shared m) -+ ENDIF() -+ -+ IF(LAPACK_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_idas_shared ${LAPACK_LIBRARIES}) -+ ENDIF() -+ -+ IF(KLU_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_idas_shared ${KLU_LIBRARIES}) -+ ENDIF() -+ - # Set the library name and make sure it is not deleted - SET_TARGET_PROPERTIES(sundials_idas_shared - PROPERTIES OUTPUT_NAME sundials_idas CLEAN_DIRECT_OUTPUT 1) diff --git a/math/sundials/files/patch-src_kinsol_CMakeLists.txt b/math/sundials/files/patch-src_kinsol_CMakeLists.txt deleted file mode 100644 index 18ee03deee25..000000000000 --- a/math/sundials/files/patch-src_kinsol_CMakeLists.txt +++ /dev/null @@ -1,21 +0,0 @@ ---- src/kinsol/CMakeLists.txt.orig 2017-11-07 23:48:14 UTC -+++ src/kinsol/CMakeLists.txt -@@ -110,6 +110,18 @@ IF(BUILD_SHARED_LIBS) - TARGET_LINK_LIBRARIES(sundials_kinsol_shared m) - ENDIF() - -+ IF(UNIX) -+ TARGET_LINK_LIBRARIES(sundials_kinsol_shared m) -+ ENDIF() -+ -+ IF(LAPACK_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_kinsol_shared ${LAPACK_LIBRARIES}) -+ ENDIF() -+ -+ IF(KLU_FOUND) -+ TARGET_LINK_LIBRARIES(sundials_kinsol_shared ${KLU_LIBRARIES}) -+ ENDIF() -+ - # Set the library name and make sure it is not deleted - SET_TARGET_PROPERTIES(sundials_kinsol_shared - PROPERTIES OUTPUT_NAME sundials_kinsol CLEAN_DIRECT_OUTPUT 1) diff --git a/math/sundials/pkg-plist b/math/sundials/pkg-plist index 0321eeacf1f5..0b3cc85473cc 100644 --- a/math/sundials/pkg-plist +++ b/math/sundials/pkg-plist @@ -1,142 +1,164 @@ include/arkode/arkode.h +include/arkode/arkode_arkstep.h include/arkode/arkode_bandpre.h include/arkode/arkode_bbdpre.h -include/arkode/arkode_direct.h -include/arkode/arkode_impl.h -include/arkode/arkode_spils.h +include/arkode/arkode_butcher.h +include/arkode/arkode_butcher_dirk.h +include/arkode/arkode_butcher_erk.h +include/arkode/arkode_erkstep.h +include/arkode/arkode_ls.h +include/arkode/arkode_mristep.h include/cvode/cvode.h include/cvode/cvode_bandpre.h include/cvode/cvode_bbdpre.h include/cvode/cvode_diag.h include/cvode/cvode_direct.h -include/cvode/cvode_impl.h +include/cvode/cvode_ls.h +include/cvode/cvode_proj.h include/cvode/cvode_spils.h include/cvodes/cvodes.h include/cvodes/cvodes_bandpre.h include/cvodes/cvodes_bbdpre.h include/cvodes/cvodes_diag.h include/cvodes/cvodes_direct.h -include/cvodes/cvodes_impl.h +include/cvodes/cvodes_ls.h include/cvodes/cvodes_spils.h include/ida/ida.h include/ida/ida_bbdpre.h include/ida/ida_direct.h -include/ida/ida_impl.h +include/ida/ida_ls.h include/ida/ida_spils.h include/idas/idas.h include/idas/idas_bbdpre.h include/idas/idas_direct.h -include/idas/idas_impl.h +include/idas/idas_ls.h include/idas/idas_spils.h include/kinsol/kinsol.h include/kinsol/kinsol_bbdpre.h include/kinsol/kinsol_direct.h -include/kinsol/kinsol_impl.h +include/kinsol/kinsol_ls.h include/kinsol/kinsol_spils.h +include/nvector/nvector_manyvector.h +%%MPI%%include/nvector/nvector_mpimanyvector.h +%%MPI%%include/nvector/nvector_mpiplusx.h %%MPI%%include/nvector/nvector_parallel.h %%HYPRE%%include/nvector/nvector_parhyp.h %%PETSC%%include/nvector/nvector_petsc.h include/nvector/nvector_pthreads.h include/nvector/nvector_serial.h +include/sundials/NOTICE include/sundials/sundials_band.h include/sundials/sundials_config.h include/sundials/sundials_dense.h include/sundials/sundials_direct.h +include/sundials/sundials_export.h include/sundials/sundials_fconfig.h include/sundials/sundials_fnvector.h +include/sundials/sundials_futils.h include/sundials/sundials_iterative.h %%LAPACK%%include/sundials/sundials_lapack.h include/sundials/sundials_linearsolver.h include/sundials/sundials_math.h include/sundials/sundials_matrix.h +include/sundials/sundials_memory.h %%MPI%%include/sundials/sundials_mpi_types.h +include/sundials/sundials_nonlinearsolver.h include/sundials/sundials_nvector.h -include/sundials/sundials_pcg.h -include/sundials/sundials_sparse.h -include/sundials/sundials_spbcgs.h -include/sundials/sundials_spfgmr.h -include/sundials/sundials_spgmr.h -include/sundials/sundials_sptfqmr.h include/sundials/sundials_types.h include/sundials/sundials_version.h include/sunlinsol/sunlinsol_band.h include/sunlinsol/sunlinsol_dense.h %%LAPACK%%include/sunlinsol/sunlinsol_lapackband.h %%LAPACK%%include/sunlinsol/sunlinsol_lapackdense.h include/sunlinsol/sunlinsol_pcg.h include/sunlinsol/sunlinsol_spbcgs.h include/sunlinsol/sunlinsol_spfgmr.h include/sunlinsol/sunlinsol_spgmr.h include/sunlinsol/sunlinsol_sptfqmr.h include/sunmatrix/sunmatrix_band.h include/sunmatrix/sunmatrix_dense.h include/sunmatrix/sunmatrix_sparse.h +include/sunnonlinsol/sunnonlinsol_fixedpoint.h +include/sunnonlinsol/sunnonlinsol_newton.h +lib/cmake/sundials/SUNDIALSConfig.cmake +lib/cmake/sundials/SUNDIALSConfigVersion.cmake +lib/cmake/sundials/SUNDIALSTargets-%%CMAKE_BUILD_TYPE%%.cmake +lib/cmake/sundials/SUNDIALSTargets.cmake lib/libsundials_arkode.so -lib/libsundials_arkode.so.2 -lib/libsundials_arkode.so.2.1.2 +lib/libsundials_arkode.so.4 +lib/libsundials_arkode.so.4.7.0 lib/libsundials_cvode.so -lib/libsundials_cvode.so.%%SHL1%% -lib/libsundials_cvode.so.%%SHL3%% +lib/libsundials_cvode.so.5 +lib/libsundials_cvode.so.5.7.0 lib/libsundials_cvodes.so -lib/libsundials_cvodes.so.%%SHL1%% -lib/libsundials_cvodes.so.%%SHL3%% +lib/libsundials_cvodes.so.5 +lib/libsundials_cvodes.so.5.7.0 +lib/libsundials_generic.so +lib/libsundials_generic.so.5 +lib/libsundials_generic.so.5.7.0 lib/libsundials_ida.so -lib/libsundials_ida.so.%%SHL1%% -lib/libsundials_ida.so.%%SHL3%% +lib/libsundials_ida.so.5 +lib/libsundials_ida.so.5.7.0 lib/libsundials_idas.so -lib/libsundials_idas.so.2 -lib/libsundials_idas.so.2.1.2 +lib/libsundials_idas.so.4 +lib/libsundials_idas.so.4.7.0 lib/libsundials_kinsol.so -lib/libsundials_kinsol.so.%%SHL1%% -lib/libsundials_kinsol.so.%%SHL3%% +lib/libsundials_kinsol.so.5 +lib/libsundials_kinsol.so.5.7.0 +lib/libsundials_nvecmanyvector.so +lib/libsundials_nvecmanyvector.so.5 +lib/libsundials_nvecmanyvector.so.5.7.0 +%%MPI%%lib/libsundials_nvecmpimanyvector.so +%%MPI%%lib/libsundials_nvecmpimanyvector.so.5 +%%MPI%%lib/libsundials_nvecmpimanyvector.so.5.7.0 +%%MPI%%lib/libsundials_nvecmpiplusx.so +%%MPI%%lib/libsundials_nvecmpiplusx.so.5 +%%MPI%%lib/libsundials_nvecmpiplusx.so.5.7.0 %%MPI%%lib/libsundials_nvecparallel.so -%%MPI%%lib/libsundials_nvecparallel.so.%%SHL1%% -%%MPI%%lib/libsundials_nvecparallel.so.%%SHL3%% +%%MPI%%lib/libsundials_nvecparallel.so.5 +%%MPI%%lib/libsundials_nvecparallel.so.5.7.0 %%HYPRE%%lib/libsundials_nvecparhyp.so -%%HYPRE%%lib/libsundials_nvecparhyp.so.%%SHL1%% -%%HYPRE%%lib/libsundials_nvecparhyp.so.%%SHL3%% +%%HYPRE%%lib/libsundials_nvecparhyp.so.5 +%%HYPRE%%lib/libsundials_nvecparhyp.so.5.7.0 %%PETSC%%lib/libsundials_nvecpetsc.so -%%PETSC%%lib/libsundials_nvecpetsc.so.%%SHL1%% -%%PETSC%%lib/libsundials_nvecpetsc.so.%%SHL3%% +%%PETSC%%lib/libsundials_nvecpetsc.so.3 +%%PETSC%%lib/libsundials_nvecpetsc.so.3.1.2 lib/libsundials_nvecpthreads.so -lib/libsundials_nvecpthreads.so.%%SHL1%% -lib/libsundials_nvecpthreads.so.%%SHL3%% +lib/libsundials_nvecpthreads.so.5 +lib/libsundials_nvecpthreads.so.5.7.0 lib/libsundials_nvecserial.so -lib/libsundials_nvecserial.so.%%SHL1%% -lib/libsundials_nvecserial.so.%%SHL3%% +lib/libsundials_nvecserial.so.5 +lib/libsundials_nvecserial.so.5.7.0 lib/libsundials_sunlinsolband.so -lib/libsundials_sunlinsolband.so.%%SHLX1%% -lib/libsundials_sunlinsolband.so.%%SHLX3%% +lib/libsundials_sunlinsolband.so.3.7.0 lib/libsundials_sunlinsoldense.so -lib/libsundials_sunlinsoldense.so.%%SHLX1%% -lib/libsundials_sunlinsoldense.so.%%SHLX3%% +lib/libsundials_sunlinsoldense.so.3.7.0 %%LAPACK%%lib/libsundials_sunlinsollapackband.so %%LAPACK%%lib/libsundials_sunlinsollapackband.so.%%SHLX1%% %%LAPACK%%lib/libsundials_sunlinsollapackband.so.%%SHLX3%% %%LAPACK%%lib/libsundials_sunlinsollapackdense.so %%LAPACK%%lib/libsundials_sunlinsollapackdense.so.%%SHLX1%% %%LAPACK%%lib/libsundials_sunlinsollapackdense.so.%%SHLX3%% lib/libsundials_sunlinsolpcg.so -lib/libsundials_sunlinsolpcg.so.%%SHLX1%% -lib/libsundials_sunlinsolpcg.so.%%SHLX3%% +lib/libsundials_sunlinsolpcg.so.3.7.0 lib/libsundials_sunlinsolspbcgs.so -lib/libsundials_sunlinsolspbcgs.so.%%SHLX1%% -lib/libsundials_sunlinsolspbcgs.so.%%SHLX3%% +lib/libsundials_sunlinsolspbcgs.so.3.7.0 lib/libsundials_sunlinsolspfgmr.so -lib/libsundials_sunlinsolspfgmr.so.%%SHLX1%% -lib/libsundials_sunlinsolspfgmr.so.%%SHLX3%% +lib/libsundials_sunlinsolspfgmr.so.3.7.0 lib/libsundials_sunlinsolspgmr.so -lib/libsundials_sunlinsolspgmr.so.%%SHLX1%% -lib/libsundials_sunlinsolspgmr.so.%%SHLX3%% +lib/libsundials_sunlinsolspgmr.so.3.7.0 lib/libsundials_sunlinsolsptfqmr.so -lib/libsundials_sunlinsolsptfqmr.so.%%SHLX1%% -lib/libsundials_sunlinsolsptfqmr.so.%%SHLX3%% +lib/libsundials_sunlinsolsptfqmr.so.3.7.0 lib/libsundials_sunmatrixband.so -lib/libsundials_sunmatrixband.so.%%SHLX1%% -lib/libsundials_sunmatrixband.so.%%SHLX3%% +lib/libsundials_sunmatrixband.so.3 +lib/libsundials_sunmatrixband.so.3.7.0 lib/libsundials_sunmatrixdense.so -lib/libsundials_sunmatrixdense.so.%%SHLX1%% -lib/libsundials_sunmatrixdense.so.%%SHLX3%% +lib/libsundials_sunmatrixdense.so.3 +lib/libsundials_sunmatrixdense.so.3.7.0 lib/libsundials_sunmatrixsparse.so -lib/libsundials_sunmatrixsparse.so.%%SHLX1%% -lib/libsundials_sunmatrixsparse.so.%%SHLX3%% +lib/libsundials_sunmatrixsparse.so.3 +lib/libsundials_sunmatrixsparse.so.3.7.0 +lib/libsundials_sunnonlinsolfixedpoint.so +lib/libsundials_sunnonlinsolfixedpoint.so.2.7.0 +lib/libsundials_sunnonlinsolnewton.so +lib/libsundials_sunnonlinsolnewton.so.2.7.0