diff --git a/biology/augustus/Makefile b/biology/augustus/Makefile index f5725eb93f47..1694ab2bd5aa 100644 --- a/biology/augustus/Makefile +++ b/biology/augustus/Makefile @@ -1,48 +1,48 @@ PORTNAME= augustus DISTVERSIONPREFIX= v DISTVERSION= 3.5.0 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= biology science PKGNAMESUFFIX= -gene-prediction MAINTAINER= yuri@FreeBSD.org COMMENT= Genome annotation tool WWW= http://bioinf.uni-greifswald.de/webaugustus/ LICENSE= GPLv3 LIB_DEPENDS= libbamtools.so:biology/bamtools \ libboost_iostreams.so:devel/boost-libs \ libcolamd.so:math/suitesparse-colamd \ libgsl.so:math/gsl \ libhts.so:biology/htslib \ liblpsolve55.so:math/lp_solve \ libmysqlpp.so:databases/mysql++ RUN_DEPENDS= samtools:biology/samtools USES= gmake localbase:ldflags mysql perl5 python sqlite shebangfix USE_CXXSTD= c++14 USE_GITHUB= yes GH_ACCOUNT= Gaius-Augustus GH_PROJECT= Augustus SHEBANG_GLOB= *.pl *.py SHEBANG_FILES= scripts/checkUTR CXXFLAGS+= -I${LOCALBASE}/include/bamtools \ -I${LOCALBASE}/include/lpsolve \ -I${LOCALBASE}/include/mysql LDFLAGS+= -L${LOCALBASE}/lib/mysql MAKE_ARGS= INSTALLDIR=${LOCALBASE}/${PORTNAME} RLN="${RLN}" BINARY_ALIAS= make=${GMAKE} python3=${PYTHON_CMD} TEST_TARGET= test post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/${PORTNAME}/bin/* @${RM} ${STAGEDIR}${PREFIX}/${PORTNAME}/scripts/pasapolyA2hints.pl.orig .include diff --git a/biology/biosig/Makefile b/biology/biosig/Makefile index f34dfee41237..5e1d2b6e50c7 100644 --- a/biology/biosig/Makefile +++ b/biology/biosig/Makefile @@ -1,42 +1,43 @@ PORTNAME= biosig DISTVERSION= 2.6.0 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= SF/${PORTNAME}/BioSig%20for%20C_C%2B%2B/src/ DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= yuri@FreeBSD.org COMMENT= Library for reading and writing different biosignal data format WWW= https://biosig.sourceforge.net/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libb64.so:converters/libb64 \ libcholmod.so:math/suitesparse-cholmod \ libiconv.so:converters/libiconv \ libtinyxml.so:textproc/tinyxml USES= gmake iconv localbase:ldflags tar:xz USE_LDCONFIG= yes WRKSRC= ${WRKDIR}/${PORTNAME}-${DISTVERSION} GNU_CONFIGURE= yes GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share CFLAGS+= -D__BYTE_ORDER=BYTE_ORDER -D__LITTLE_ENDIAN=LITTLE_ENDIAN -D__BIG_ENDIAN=BIG_ENDIAN \ -Dbswap_16=bswap16 -Dbswap_32=bswap32 -Dbswap_64=bswap64 LDFLAGS+= -liconv .include .if ${OPSYS} == FreeBSD && ( ${OSVERSION} >= 1400079 || ( ${OSVERSION} >= 1302505 && ${OSVERSION} < 1400000 )) CFLAGS+= -Wno-error=int-conversion .endif post-install: .for f in bin/biosig_fhir bin/biosig2gdf bin/physicalunits bin/save2gdf lib/libbiosig.so.3 @${STRIP_CMD} ${STAGEDIR}${PREFIX}/${f} .endfor .include diff --git a/cad/xyce/Makefile b/cad/xyce/Makefile index c116ec01de24..7ba15d45ac1d 100644 --- a/cad/xyce/Makefile +++ b/cad/xyce/Makefile @@ -1,76 +1,76 @@ PORTNAME= xyce DISTVERSIONPREFIX= Release- DISTVERSION= 7.8.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= cad MAINTAINER= yuri@FreeBSD.org COMMENT= Xyce electronic simulator WWW= https://xyce.sandia.gov/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libblas.so:math/blas \ libfftw3.so:math/fftw3 \ liblapack.so:math/lapack \ libtpetra.so:science/trilinos \ \ libamd.so:math/suitesparse-amd \ libcholmod.so:math/suitesparse-cholmod \ libcolamd.so:math/suitesparse-colamd \ libsuitesparseconfig.so:math/suitesparse-config \ libumfpack.so:math/suitesparse-umfpack TEST_DEPENDS= git:devel/git \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} USES= autoreconf bison gmake fortran libtool localbase perl5 python:test # GNU tools should be used for 7.5 and on until the cmake build is declared stable USE_CXXSTD= c++14 # otherwise configure fails because of c++14 features like std::conditional_t USE_CXXSTD= c++17 # workaround for https://github.com/Xyce/Xyce/issues/97, which occurred when Trilinos was updated to 15.1.0 USE_LDCONFIG= yes USE_PERL5= test USE_GITHUB= yes GH_ACCOUNT= Xyce GH_PROJECT= Xyce GNU_CONFIGURE= yes CONFIGURE_ARGS= LEX=/usr/bin/flex \ --enable-stokhos \ --enable-amesos \ --enable-shared \ --disable-static INSTALL_TARGET= install-strip BINARY_ALIAS= python=${PYTHON_CMD} # only for tests do-test: # one test is known to fail, see https://github.com/Xyce/Xyce/issues/67#issuecomment-1179857728 # checkout tests @cd ${WRKDIR} && \ ${ECHO} "cloning git repository ..." && \ ${RM} -rf Xyce_Regression && \ git clone -q https://github.com/Xyce/Xyce_Regression.git && \ cd Xyce_Regression && \ git checkout -q Release-${DISTVERSION} # run tests @cd ${TEST_WRKSRC} && ( \ ${ECHO} "running tests ..."; \ eval `${WRKDIR}/Xyce_Regression/TestScripts/suggestXyceTagList.sh ${STAGEDIR}${PREFIX}/bin/Xyce` ; \ ${SETENV} ${TEST_ENV} ${WRKDIR}/Xyce_Regression/TestScripts/run_xyce_regression \ --output=${WRKDIR}/Xyce_Test \ --xyce_test="${WRKDIR}/Xyce_Regression" \ --resultfile=${WRKDIR}/serial_results \ --taglist="$$TAGLIST" \ ${STAGEDIR}${PREFIX}/bin/Xyce \ ) # Testssuite doesn't stop when Ctrl-C is pressed: https://github.com/Xyce/Xyce_Regression/issues/1 # Trilinos build instructions for Xyce: https://xyce.sandia.gov/documentation-tutorials/building-guide/#instTrilinos # Xyce build instructions: https://xyce.sandia.gov/documentation-tutorials/building-guide/ # Xyce regression suite instructions: https://xyce.sandia.gov/documentation-tutorials/running-the-xyce-regression-suite/ # docs are in https://xyce.sandia.gov/files/xyce/Xyce_Docs-7.5.tar.gz .include diff --git a/games/naev/Makefile b/games/naev/Makefile index 2b5e03d6c2cb..5eee1b316be9 100644 --- a/games/naev/Makefile +++ b/games/naev/Makefile @@ -1,52 +1,52 @@ PORTNAME= naev PORTVERSION= 0.10.6 DISTVERSIONSUFFIX= -source -PORTREVISION= 12 +PORTREVISION= 13 CATEGORIES= games MASTER_SITES= https://github.com/naev/naev/releases/download/v${PORTVERSION}/ MAINTAINER= acm@FreeBSD.org COMMENT= 2D action/RPG space game WWW= https://naev.org/ LICENSE= GPLv2 GPLv3 CC-BY-3.0 CC-BY-SA-3.0 PD LICENSE_COMB= multi BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mutagen>0:audio/py-mutagen@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libbacktrace.so:devel/libbacktrace \ libblas.so:math/blas \ libcholmod.so:math/suitesparse-cholmod \ libcolamd.so:math/suitesparse-colamd \ libcxsparse.so:math/suitesparse-cxsparse \ libenet.so:net/enet \ libfreetype.so:print/freetype2 \ libglpk.so:math/glpk \ libopenblas.so:math/openblas \ libpcre2-8.so:devel/pcre2 \ libphysfs.so:devel/physfs \ libpng.so:graphics/png \ libunibreak.so:textproc/libunibreak \ libvorbisfile.so:audio/libvorbis \ libwebp.so:graphics/webp \ libzip.so:archivers/libzip RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}mutagen>0:audio/py-mutagen@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} USES= desktop-file-utils gettext gl gnome localbase:ldflags \ luajit:luajit-openresty meson openal pkgconfig python sdl \ shebangfix tar:xz USE_GL= gl glu USE_GNOME= intltool libxml2 USE_SDL= sdl2 image2 SHEBANG_GLOB= *.py *.sh MESON_ARGS= -Ddocs_c=disabled -Ddocs_lua=disabled BINARY_ALIAS= python3=${PYTHON_CMD} WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} .include diff --git a/graphics/libpano13/Makefile b/graphics/libpano13/Makefile index dbb13e0a260b..884b1390c29b 100644 --- a/graphics/libpano13/Makefile +++ b/graphics/libpano13/Makefile @@ -1,36 +1,36 @@ PORTNAME= libpano13 DISTVERSION= 2.9.22 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= graphics java MASTER_SITES= SF/panotools/${PORTNAME}/${PORTNAME}-${DISTVERSION} MAINTAINER= fuz@FreeBSD.org COMMENT= Cross-platform library behind Panorama Tools and other photo stitchers WWW= https://panotools.sourceforge.net/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libpng.so:graphics/png \ libtiff.so:graphics/tiff USES= cmake:testing cpe jpeg libtool pathfix perl5 pkgconfig CPE_VENDOR= ${PORTNAME}_project USE_LDCONFIG= yes USE_PERL5= build # for pod2man WRKSRC= ${WRKDIR}/libpano13-${DISTVERSION} OPTIONS_DEFINE= DOCS JAVA SUITESPARSE OPTIONS_DEFAULT= SUITESPARSE SUITESPARSE_DESC= Use math/suitesparse for faster operation OPTIONS_SUB= yes JAVA_USE= java=yes JAVA_CMAKE_BOOL= SUPPORT_JAVA_PROGRAMS JAVA_VARS= JAVA_OS=native SUITESPARSE_LIB_DEPENDS= \ libcholmod.so:math/suitesparse-cholmod \ libspqr.so:math/suitesparse-spqr SUITESPARSE_CMAKE_BOOL= USE_SPARSE_LEVMAR .include diff --git a/math/arpack++/Makefile b/math/arpack++/Makefile index 6eb310df9a4c..744f30dbb166 100644 --- a/math/arpack++/Makefile +++ b/math/arpack++/Makefile @@ -1,65 +1,65 @@ PORTNAME= arpack++ PORTVERSION= 2.4.0 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= math MAINTAINER= ports@FreeBSD.org COMMENT= Object-oriented version of the ARPACK package WWW= https://www.ime.unicamp.br/~chico/arpack++/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libarpack.so:math/arpack-ng \ libsuperlu.so:math/superlu \ libcholmod.so:math/suitesparse-cholmod \ libumfpack.so:math/suitesparse-umfpack USES= cmake:testing compiler:c++17-lang fortran USE_CXXSTD= c++17 USE_GITHUB= yes GH_ACCOUNT= m-reuter GH_PROJECT= arpackpp CMAKE_ARGS= -DENABLE_FORTRAN:BOOL=ON \ -DENABLE_SUPERLU:BOOL=ON \ -DENABLE_UMFPACK:BOOL=ON \ -DENABLE_CHOLMOD:BOOL=ON \ -DENABLE_SUITESPARSE_STATIC:BOOL=OFF NO_ARCH= yes REINPLACE_ARGS= -i "" DOCS= README.md doc/README doc/arpackpp.pdf doc/structure.txt OPTIONS_DEFINE= DOCS EXAMPLES OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= ATLAS NETLIB OPENBLAS OPTIONS_DEFAULT= OPENBLAS EXAMPLES_CMAKE_ON= -DENABLE_TESTS:BOOL=ON EXAMPLES_CMAKE_OFF= -DENABLE_TESTS:BOOL=OFF EXAMPLES_VARS_OFF= NO_BUILD=yes ATLAS_USES= blaslapack:atlas NETLIB_USES= blaslapack:netlib OPENBLAS_USES= blaslapack:openblas PORTDOCS= * PORTEXAMPLES= * do-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} .for doc in ${DOCS} ${INSTALL_DATA} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} .endfor @${ECHO_MSG} "===> Documentation installed in ${DOCSDIR}." do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} @${ECHO_MSG} "===> Examples installed in ${EXAMPLESDIR}." .include diff --git a/math/ceres-solver/Makefile b/math/ceres-solver/Makefile index 8c1811ee432f..885acd0a6365 100644 --- a/math/ceres-solver/Makefile +++ b/math/ceres-solver/Makefile @@ -1,112 +1,112 @@ PORTNAME= ceres-solver DISTVERSION= 2.2.0 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Nonlinear least squares minimizer WWW= http://ceres-solver.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_armv7= compilation fails, gcc-13 fails with the error: use of built-in trait '__remove_cvref(_Tp)' in function signature; use library traits instead, see https://pkg-status.freebsd.org/ampere3/data/140releng-armv7-default/26c5fe5d2fe6/logs/ceres-solver-2.2.0_8.log BUILD_DEPENDS= glog>=0.5.0:devel/glog LIB_DEPENDS= libglog.so:devel/glog RUN_DEPENDS:= ${BUILD_DEPENDS:Meigen*} USES= cmake:testing compiler:${OPENMP}c++11-lib eigen:3 localbase shebangfix USE_GITHUB= yes USE_LDCONFIG= yes SHEBANG_FILES= examples/slam/pose_graph_*/plot_results.py \ scripts/make_docs.py CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= BUILD_BENCHMARKS BUILD_TESTING LDFLAGS+= -Wl,--as-needed # -lccolamd -lcholmod -lrt from suitesparse PLIST_SUB= VERSION=${DISTVERSION:C/rc.*//} EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME:S/-solver//} DOCSDIR= ${PREFIX}/share/doc/Ceres PORTDOCS= * PORTEXAMPLES= * OPTIONS_DEFINE= CUSTOM_BLAS EXAMPLES DOCS GFLAGS LAPACK OPENMP SCHUR OPTIONS_DEFAULT= CUSTOM_BLAS CXSPARSE GFLAGS OPENBLAS OPENMP SCHUR SUITESPARSE OPTIONS_RADIO= LAPACK THREADS OPTIONS_RADIO_LAPACK= ATLAS NETLIB OPENBLAS OPTIONS_GROUP= SPARSE OPTIONS_GROUP_SPARSE= CXSPARSE EIGENSPARSE SUITESPARSE CUSTOM_BLAS_DESC= Handcoded BLAS routines instead of Eigen CUSTOM_BLAS_CMAKE_BOOL= CUSTOM_BLAS DOCS_BUILD_DEPENDS= sphinx-build:textproc/py-sphinx \ ${PYTHON_PKGNAMEPREFIX}sphinx_rtd_theme>0:textproc/py-sphinx_rtd_theme@${PY_FLAVOR} DOCS_USES= python:build DOCS_CMAKE_BOOL= BUILD_DOCUMENTATION EXAMPLES_CMAKE_BOOL= BUILD_EXAMPLES EXAMPLES_IMPLIES= GFLAGS GFLAGS_DESC= Google Flags support GFLAGS_LIB_DEPENDS= libgflags.so:devel/gflags GFLAGS_CMAKE_BOOL= GFLAGS OPENMP_CMAKE_ON= -DCERES_THREADING_MODEL:STRING="OPENMP" .if !exists(/usr/include/omp.h) # XXX ports/199603: LLVM openmp in base doesn't support armv6, armv7 yet OPENMP_VARS= OPENMP=gcc- .endif SCHUR_DESC= Fixed-size schur specializations SCHUR_CMAKE_BOOL= SCHUR_SPECIALIZATIONS # XXX Unbundle googletest/googlemock LAPACK_DESC= Linear Algebra PACKage LAPACK_CMAKE_BOOL= LAPACK ATLAS_USES= blaslapack:atlas ATLAS_CMAKE_ON= -DBLA_VENDOR:STRING="ATLAS" \ -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libcblas.so" \ -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libalapack.so" ATLAS_IMPLIES= LAPACK NETLIB_USES= blaslapack:netlib NETLIB_CMAKE_ON= -DBLA_VENDOR:STRING="Generic" NETLIB_IMPLIES= LAPACK OPENBLAS_USES= blaslapack:openblas OPENBLAS_CMAKE_ON= -DBLA_VENDOR:STRING="OpenBLAS" OPENBLAS_IMPLIES= LAPACK SPARSE_DESC= Sparse linear algebra library CXSPARSE_DESC= CXSparse support CXSPARSE_LIB_DEPENDS= libcxsparse.so:math/suitesparse-cxsparse CXSPARSE_CMAKE_ON= -DCXSPARSE_INCLUDE_DIR:PATH="${LOCALBASE}/include/suitesparse" CXSPARSE_CMAKE_BOOL= CXSPARSE EIGENSPARSE_DESC= Simplicial Cholesky factorization in Eigen EIGENSPARSE_CMAKE_BOOL= EIGENSPARSE EIGENSPARSE_VARS= LICENSE+=LGPL21+ LICENSE_COMB=multi \ LICENSE_FILE_BSD3CLAUSE="${LICENSE_FILE}" SUITESPARSE_DESC= SuiteSparse support SUITESPARSE_LIB_DEPENDS=libspqr.so:math/suitesparse-spqr \ libcholmod.so:math/suitesparse-cholmod SUITESPARSE_CMAKE_BOOL= SUITESPARSE post-patch-DOCS-on: @${REINPLACE_CMD} -e 's,python,${PYTHON_CMD:T},' \ ${WRKSRC}/docs/source/CMakeLists.txt pre-install-TEST-on: do-test post-install-EXAMPLES-on: # Copy examples (stripped), their source and sample data but not tests programs (cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) (cd ${WRKSRC} && ${COPYTREE_SHARE} data ${STAGEDIR}${EXAMPLESDIR}) (cd ${BUILD_WRKSRC} && ${COPYTREE_SHARE} bin ${STAGEDIR}${EXAMPLESDIR}) @${RM} -r ${STAGEDIR}${EXAMPLESDIR}/bin/*_test -@${STRIP_CMD} ${STAGEDIR}${EXAMPLESDIR}/bin/* # may fail for non-root .include diff --git a/math/dune-fem/Makefile b/math/dune-fem/Makefile index 0d9cf9aea5b7..348853c2be27 100644 --- a/math/dune-fem/Makefile +++ b/math/dune-fem/Makefile @@ -1,68 +1,68 @@ PORTNAME= dune-fem DISTVERSION= 2.8.0.5 -PORTREVISION= 21 +PORTREVISION= 22 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: Finite Element Methods, Finite Volume Methods, etc WWW= https://www.dune-project.org/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.md BUILD_DEPENDS= arpack++>0:math/arpack++ \ dune-istl>=2.6:math/dune-istl \ dune-localfunctions>=2.6:math/dune-localfunctions \ dune-spgrid>0:math/dune-spgrid \ vc>0:devel/vc \ openmpi4>0:net/openmpi4 LIB_DEPENDS= libpsurface.so:math/psurface \ libarpack.so:math/arpack-ng \ libdunealugrid.so:math/dune-alugrid \ libdunecommon.so:math/dune-common \ libdunegeometry.so:math/dune-geometry \ libdunegrid.so:math/dune-grid \ libdunepolygongrid.so:math/dune-polygongrid \ libduneuggrid.so:math/dune-uggrid \ libgmp.so:math/gmp \ libmetis.so:math/metis \ libopenblas.so:math/openblas \ libsuitesparseconfig.so:math/suitesparse-config \ libsuperlu.so:math/superlu \ 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 \ libldl.so:math/suitesparse-ldl \ libspqr.so:math/suitesparse-spqr \ libumfpack.so:math/suitesparse-umfpack \ libtbb.so:devel/onetbb RUN_DEPENDS= dune-istl>=2.6:math/dune-istl \ dune-localfunctions>=2.6:math/dune-localfunctions \ dune-spgrid>0:math/dune-spgrid \ openmpi4>0:net/openmpi4 USES= cmake compiler:c++17-lang eigen:3 fortran pkgconfig USE_GITLAB= yes USE_LDCONFIG= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= dune-fem GL_TAGNAME= 30e278aa744c908fbf4bbd8b237eb26c0475d16e CMAKE_ON= BUILD_SHARED_LIBS OPTIONS_DEFINE= DOCS DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ sphinx-build:textproc/py-sphinx PORTDOCS= * post-install: # https://gitlab.dune-project.org/dune-fem/dune-fem/-/issues/111 ${RM} ${STAGEDIR}${PREFIX}/share/dune/cmake/modules/FindPThreads.cmake ${RM} ${STAGEDIR}${PREFIX}/share/dune/cmake/modules/FindSIONlib.cmake .include diff --git a/math/dune-istl/Makefile b/math/dune-istl/Makefile index 1ba733d48198..e05531f474c4 100644 --- a/math/dune-istl/Makefile +++ b/math/dune-istl/Makefile @@ -1,41 +1,41 @@ PORTNAME= dune-istl DISTVERSION= 2.8.0 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: Iterative Solver Template Library WWW= https://www.dune-project.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE.md HPP_DEPENDS= arpack++>0:math/arpack++ \ dune-common>0:math/dune-common \ suitesparse>0:math/suitesparse # needed in headers, but OPTIONAL dependency set is wider: https://gitlab.dune-project.org/core/dune-istl/-/issues/97 BUILD_DEPENDS= ${HPP_DEPENDS} \ vc>0:devel/vc RUN_DEPENDS= ${HPP_DEPENDS} USES= cmake compiler:c++17-lang fortran pkgconfig USE_GITLAB= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= core GL_TAGNAME= fffb544a61d2c65a0d2fc7c751f36909f06be8f5 NO_ARCH= yes OPTIONS_DEFINE= DOCS PARMETIS OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ PARMETIS_DESC= Install PerMetis # needed in headers, but license prohibits packaging PARMETIS_BUILD_DEPENDS= ParMetis>0:math/parmetis PARMETIS_RUN_DEPENDS= ParMetis>0:math/parmetis PORTDOCS= * .include diff --git a/math/dune-pdelab/Makefile b/math/dune-pdelab/Makefile index 266d80ec4dc5..aa99310dc8b7 100644 --- a/math/dune-pdelab/Makefile +++ b/math/dune-pdelab/Makefile @@ -1,66 +1,66 @@ PORTNAME= dune-pdelab DISTVERSIONPREFIX= v DISTVERSION= 2.7.0.20210824 -PORTREVISION= 22 +PORTREVISION= 23 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: PDE solver toolbox WWW= https://www.dune-project.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING DUNE_DEPENDS= dune-common>0:math/dune-common \ dune-functions>0:math/dune-functions \ dune-grid>0:math/dune-grid \ dune-istl>0:math/dune-istl \ dune-geometry>0:math/dune-geometry \ dune-localfunctions>0:math/dune-localfunctions \ dune-typetree>0:math/dune-typetree BUILD_DEPENDS= ${DUNE_DEPENDS} \ suitesparse>0:math/suitesparse \ openmpi4>0:net/openmpi4 LIB_DEPENDS= libarpack.so:math/arpack-ng \ libdunealugrid.so:math/dune-alugrid \ libduneuggrid.so:math/dune-uggrid \ libgmp.so:math/gmp \ libmetis.so:math/metis \ libpsurface.so:math/psurface \ libopenblas.so:math/openblas \ 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 \ libldl.so:math/suitesparse-ldl \ libspqr.so:math/suitesparse-spqr \ libumfpack.so:math/suitesparse-umfpack \ libsuperlu.so:math/superlu \ libtbb.so:devel/onetbb RUN_DEPENDS= ${DUNE_DEPENDS} \ suitesparse>0:math/suitesparse \ openmpi4>0:net/openmpi4 USES= cmake compiler:c++17-lang fortran pkgconfig USE_GITLAB= yes USE_LDCONFIG= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= pdelab GL_TAGNAME= 20c7085389d3eb4f8ca99e1bc60f7fa6036536c8 CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DTBB_INCLUDE_DIR=${LOCALBASE}/include -DTBB_LIBRARIES=${LOCALBASE}/lib/libtbb.so OPTIONS_DEFINE= DOCS OPTIONS_SUB= yes DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ sphinx-build:textproc/py-sphinx PORTDOCS= * .include diff --git a/math/dune-vtk/Makefile b/math/dune-vtk/Makefile index b2a03fc94245..7a1432cb5cb0 100644 --- a/math/dune-vtk/Makefile +++ b/math/dune-vtk/Makefile @@ -1,63 +1,63 @@ PORTNAME= dune-vtk DISTVERSION= 2.8.0 -PORTREVISION= 20 +PORTREVISION= 21 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= DUNE framework: File reader and writer for the VTK XML format WWW= https://www.dune-project.org/ LICENSE= GPLv2+ HPP_DEPENDS= ${LOCALBASE}/include/dune/foamgrid/foamgrid.hh:math/dune-foamgrid \ dune-localfunctions>0:math/dune-localfunctions \ dune-spgrid>0:math/dune-spgrid BUILD_DEPENDS= ${HPP_DEPENDS} \ dune-functions>0:math/dune-functions \ suitesparse>0:math/suitesparse \ openmpi4>0:net/openmpi4 LIB_DEPENDS= libarpack.so:math/arpack-ng \ libdunealugrid.so:math/dune-alugrid \ libdunecommon.so:math/dune-common \ libdunegeometry.so:math/dune-geometry \ libdunegrid.so:math/dune-grid \ libdunepolygongrid.so:math/dune-polygongrid \ libduneuggrid.so:math/dune-uggrid \ libgmp.so:math/gmp \ libmetis.so:math/metis \ libopenblas.so:math/openblas \ libpsurface.so:math/psurface \ 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 \ libldl.so:math/suitesparse-ldl \ libspqr.so:math/suitesparse-spqr \ libumfpack.so:math/suitesparse-umfpack \ libsuperlu.so:math/superlu \ libtbb.so:devel/onetbb RUN_DEPENDS= ${HPP_DEPENDS} \ suitesparse>0:math/suitesparse \ openmpi4>0:net/openmpi4 USES= cmake compiler:c++17-lang fortran pkgconfig USE_GITLAB= yes USE_LDCONFIG= yes GL_SITE= https://gitlab.dune-project.org GL_ACCOUNT= extensions GL_TAGNAME= 467838cde3bbea3d27d2bd117570a3215240dcd1 CMAKE_ON= BUILD_SHARED_LIBS OPTIONS_DEFINE= DOCS DOCS_CMAKE_BOOL= FREEBSD_INSTALL_DOCS DOCS_BUILD_DEPENDS= doxygen:devel/doxygen \ sphinx-build:textproc/py-sphinx PORTDOCS= * .include diff --git a/math/freefem++/Makefile b/math/freefem++/Makefile index 73fd957ac85d..b92e61b45828 100644 --- a/math/freefem++/Makefile +++ b/math/freefem++/Makefile @@ -1,76 +1,76 @@ PORTNAME= freefem++ DISTVERSIONPREFIX= v DISTVERSION= 4.14 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= math science MAINTAINER= yuri@FreeBSD.org COMMENT= Partial differential equation solver WWW= https://freefem.org/index.html LICENSE= LGPL3 BUILD_DEPENDS= bash:shells/bash \ gmm++>0:math/gmm++ \ pipe:misc/pipe \ tetgen:math/tetgen LIB_DEPENDS= libhdf5.so:science/hdf5 \ libamd.so:math/suitesparse-amd \ libcholmod.so:math/suitesparse-cholmod \ libcolamd.so:math/suitesparse-colamd \ libumfpack.so:math/suitesparse-umfpack \ libarpack.so:math/arpack-ng \ libfftw3.so:math/fftw3 \ libgsl.so:math/gsl \ libipopt.so:math/ipopt \ libmetis.so:math/metis \ libscotch.so:cad/scotch \ libcmumps.so:math/mumps \ libnlopt.so:math/nlopt \ libsuperlu.so:math/superlu RUN_DEPENDS= bash:shells/bash \ pipe:misc/pipe USES= autoreconf bison blaslapack:openblas compiler:c++14-lang fortran \ gl gmake localbase perl5 pkgconfig shebangfix xorg USE_GITHUB= yes GH_ACCOUNT= FreeFem GH_PROJECT= FreeFem-sources SHEBANG_GLOB= ff-pkg-download.in SHEBANG_FILES= examples/CheckAllEdp ./examples/misc/speedtest.sh CPPFLAGS+= -I${LOCALBASE}/include/superlu .if !defined{WITH_DEBUG} LDFLAGS+= -s .endif LDFLAGS+= -pthread # workaround for https://github.com/FreeFem/FreeFem-sources/issues/296#issuecomment-1839198380 GNU_CONFIGURE= yes CONFIGURE_ENV= CNOFLAGS="${CFLAGS}" LIBS=-lz CONFIGURE_ARGS= --disable-download \ --without-mpi \ --with-blas=${BLASLIB} \ --with-lapack=${LAPACKLIB} USE_GL= gl glu glut OPTIONS_DEFINE= EXAMPLES OPTIONS_DEFAULT=EXAMPLES PORTEXAMPLES= * PLIST_SUB= VER=${PORTVERSION} DATADIR= ${PREFIX}/share/FreeFEM/${PORTVERSION} TEST_TARGET= check # 1 test fails, see https://github.com/FreeFem/FreeFem-sources/issues/281 pre-configure: @${REINPLACE_CMD} -e 's|-llapack|${LAPACKLIB}|' ${WRKSRC}/configure.ac post-install: @${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/math/g2o/Makefile b/math/g2o/Makefile index 8dc49a0a9ddd..4517205893df 100644 --- a/math/g2o/Makefile +++ b/math/g2o/Makefile @@ -1,74 +1,74 @@ PORTNAME= g2o DISTVERSION= 20230806 -PORTREVISION= 10 +PORTREVISION= 11 DISTVERSIONSUFFIX= _git CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= General framework for graph optimization WWW= https://openslam-org.github.io/g2o.html LICENSE= LGPL3 GPLv3 LICENSE_COMB= dual LIB_DEPENDS= 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 \ libcxsparse.so:math/suitesparse-cxsparse \ libQGLViewer.so:graphics/libQGLViewer \ libmetis.so:math/metis \ libopenblas.so:math/openblas \ libsuitesparseconfig.so:math/suitesparse-config TEST_DEPENDS= googletest>0:devel/googletest USES= cmake:testing compiler:c++14-lang gl eigen:3 blaslapack:netlib localbase qt:5 USE_GL= gl glu USE_QT= core gui opengl xml widgets buildtools:build qmake:build USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= RainerKuemmerle CMAKE_OFF= DO_SSE_AUTODETECT CMAKE_TESTING_ON= BUILD_UNITTESTS OPTIONS_DEFINE= FAST_MATH OPTIONS_SINGLE= SIMD_${ARCH:tu} OPTIONS_SINGLE_SIMD_AMD64= NOSSE SSE2 SSE3 SSE41 SSE42 SSE4A OPTIONS_SINGLE_SIMD_I386= ${OPTIONS_SINGLE_SIMD_AMD64} OPTIONS_DEFAULT_amd64= SSE2 OPTIONS_DEFAULT_i386= SSE2 SIMD_AMD64_DESC= Use SSE SIMD optimizations SIMD_I386_DESC= ${SIMD_AMD64_DESC} FAST_MATH_DESC= Enable fast math operations NOSSE_DESC= Do not use SIMD optimization SSE2_DESC= SSE2 optimization SSE3_DESC= SSE3 optimization SSE41_DESC= SSE41 optimization SSE42_DESC= SSE42 optimization SSE4A_DESC= SSE4a optimization FAST_MATH_CMAKE_BOOL= G2O_FAST_MATH NOSSE_CMAKE_ON= -DDISABLE_SSE2:BOOL=ON -DDISABLE_SSE3:BOOL=ON -DDISABLE_SSE4_1:BOOL=ON -DDISABLE_SSE4_2:BOOL=ON -DDISABLE_SSE4_A:BOOL=ON SSE2_CMAKE_ON= -DDISABLE_SSE3:BOOL=ON -DDISABLE_SSE4_1:BOOL=ON -DDISABLE_SSE4_2:BOOL=ON -DDISABLE_SSE4_A:BOOL=ON SSE3_CMAKE_ON= -DDISABLE_SSE4_1:BOOL=ON -DDISABLE_SSE4_2:BOOL=ON -DDISABLE_SSE4_A:BOOL=ON SSE41_CMAKE_ON= -DDISABLE_SSE4_2:BOOL=ON -DDISABLE_SSE4_A:BOOL=ON SSE42_CMAKE_ON= -DDISABLE_SSE4_A:BOOL=ON SSE4A_CMAKE_ON= # empty to make portlint happy .include .if ${ARCH} != amd64 && ${ARCH} != i386 CMAKE_ARGS+= -DDISABLE_SSE2:BOOL=ON -DDISABLE_SSE3:BOOL=ON -DDISABLE_SSE4_1:BOOL=ON -DDISABLE_SSE4_2:BOOL=ON -DDISABLE_SSE4_A:BOOL=ON .endif post-patch: @${REINPLACE_CMD} -e 's|/usr/include|${LOCALBASE}/include|' \ ${WRKSRC}/cmake_modules/*.cmake # tests fail to compile, see https://github.com/RainerKuemmerle/g2o/issues/711 .include diff --git a/math/igraph/Makefile b/math/igraph/Makefile index 9e115a7d1939..08d74f32c3e7 100644 --- a/math/igraph/Makefile +++ b/math/igraph/Makefile @@ -1,33 +1,33 @@ PORTNAME= igraph DISTVERSION= 0.10.6 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= math MASTER_SITES= https://github.com/${PORTNAME}/${PORTNAME}/releases/download/${DISTVERSION}/ MAINTAINER= wen@FreeBSD.org COMMENT= Package For Manipulating Undirected And Directed Graphs WWW= https://igraph.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/bin/flex:textproc/flex LIB_DEPENDS= libarpack.so:math/arpack-ng \ libcxsparse.so:math/suitesparse-cxsparse \ libglpk.so:math/glpk \ libgmp.so:math/gmp \ libopenblas.so:math/openblas USES= bison cmake cpe gnome pathfix USE_GNOME= libxml2 USE_LDCONFIG= yes CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= BUILD_TESTING CMAKE_ARGS= -DCMAKE_DISABLE_FIND_PACKAGE_Git:BOOL=True \ -DFLEX_EXECUTABLE:FILEPATH=${LOCALBASE}/bin/flex pre-configure: @${ECHO} ${DISTVERSION} > ${WRKSRC}/IGRAPH_VERSION .include diff --git a/math/octave/Makefile b/math/octave/Makefile index 580a280444fb..a9b864e8e25c 100644 --- a/math/octave/Makefile +++ b/math/octave/Makefile @@ -1,130 +1,131 @@ PORTNAME= octave PORTVERSION= ${OCTAVE_VERSION} +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= GNU MAINTAINER= stephen@FreeBSD.org COMMENT= High-level interactive language for numerical computations WWW= https://www.octave.org/ LICENSE= GPLv3 BUILD_DEPENDS= ${LOCALBASE}/bin/gperf:devel/gperf \ ${LOCALBASE}/bin/makeinfo:print/texinfo \ gnuplot:math/gnuplot \ gsed:textproc/gsed \ ${LOCALBASE}/include/rapidjson/rapidjson.h:devel/rapidjson RUN_DEPENDS= ${LOCALBASE}/bin/makeinfo:print/texinfo \ gnuplot:math/gnuplot \ gsed:textproc/gsed LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libarpack.so:math/arpack-ng \ libcamd.so:math/suitesparse-camd \ libccolamd.so:math/suitesparse-ccolamd \ libcholmod.so:math/suitesparse-cholmod \ libcolamd.so:math/suitesparse-colamd \ libcurl.so:ftp/curl \ libcxsparse.so:math/suitesparse-cxsparse \ libdrm.so:graphics/libdrm \ libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float \ libfltk.so:x11-toolkits/fltk \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libftgl.so:graphics/ftgl \ libgl2ps.so:print/gl2ps \ libglpk.so:math/glpk \ libGraphicsMagick.so:graphics/GraphicsMagick \ libhdf5.so:science/hdf5 \ libklu.so:math/suitesparse-klu \ libOSMesa.so:graphics/libosmesa \ libpcre.so:devel/pcre \ libportaudio.so:audio/portaudio \ libqhull_r.so:math/qhull \ libqrupdate.so:math/qrupdate \ libspqr.so:math/suitesparse-spqr \ libsuitesparseconfig.so:math/suitesparse-config \ libsundials_arkode.so:math/sundials \ libumfpack.so:math/suitesparse-umfpack USES= charsetfix compiler:c++14-lang desktop-file-utils fortran gl \ gmake iconv libtool localbase:ldflags ncurses octave:env perl5 \ pkgconfig readline tar:xz xorg USE_LDCONFIG= ${PREFIX}/lib/${PORTNAME}/${PORTVERSION} USE_PERL5= build GNU_CONFIGURE= yes USE_QT= core gui help network opengl printsupport sql widgets xml \ buildtools:build linguist:build qmake:build USE_XORG= x11 xcursor xext xfixes xft xinerama xrender USE_GL= gl glu GNU_HOST= ${ARCH}-portbld-freebsd${OSREL} PLIST_SUB= GNU_HOST=${GNU_HOST} \ OCTAVE_VERSION=${OCTAVE_VERSION} LDFLAGS+= -L${LOCALBASE}/lib/qt5 CONFIGURE_ENV= ac_cv_path_SED=${LOCALBASE}/bin/gsed \ ac_cv_type_max_align_t=yes \ GPERF="${LOCALBASE}/bin/gperf" \ JAVA_HOME=${JAVA_HOME} \ LRELEASE_QTVER=${LRELEASE} \ MAKEINFO=${LOCALBASE}/bin/makeinfo \ MKINFO=${LOCALBASE}/bin/makeinfo \ MOC_QTVER=${MOC} \ QCOLLECTIONGENERATOR_QTVER=${QCOLLECTIONGENERATOR} \ QHELPGENERATOR_QTVER=${QHELPGENERATOR} \ RCC_QTVER=${RCC} \ UIC_QTVER=${UIC} \ man1dir=${PREFIX}/share/man/man1 CONFIGURE_ARGS= --disable-jit \ --disable-openmp \ --enable-shared \ --host=${GNU_HOST} \ --with-blas="-L${LOCALBASE}/lib ${BLASLIB}" \ --with-lapack="${LAPACKLIB}" \ --with-osmesa INFO= octave liboctave INSTALL_TARGET= install-strip TEST_TARGET= check OPTIONS_DEFINE= DOCS JAVA QT5 OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= ATLAS NETLIB OPENBLAS OPTIONS_DEFAULT= JAVA OPENBLAS QT5 OPTIONS_SUB= yes DOCS_CONFIGURE_ENABLE= docs JAVA_CONFIGURE_ENABLE= java QT5_CONFIGURE_WITH= qscintilla qt=5 QT5_LIB_DEPENDS= libqscintilla2_qt5.so:devel/qscintilla2-qt5 DOCS_USES= tex DOCS_USE= TEX=dvipsk:build,formats:build JAVA_USE= JAVA=yes JAVA_CFLAGS= -I${JAVA_HOME}/include/${OPSYS:tl} QT5_USES= qt:5 OPENBLAS_USES= blaslapack:openblas NETLIB_USES= blaslapack:netlib ATLAS_USES= blaslapack:atlas BINARY_ALIAS= sed=gsed 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 diff --git a/math/openturns/Makefile b/math/openturns/Makefile index b538e749826c..c414bbfe5960 100644 --- a/math/openturns/Makefile +++ b/math/openturns/Makefile @@ -1,99 +1,99 @@ PORTNAME= openturns DISTVERSIONPREFIX= v DISTVERSION= 1.22 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Uncertainty treatment library WWW= https://openturns.github.io/www/ LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/COPYING.LESSER BUILD_DEPENDS= boost-libs>0:devel/boost-libs \ flex:textproc/flex \ spectra>0:math/spectra LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libblas.so:math/blas \ libbonmin.so:math/bonmin \ libboost_serialization.so:devel/boost-libs \ libcamd.so:math/suitesparse-camd \ libceres.so:math/ceres-solver \ libCbc.so:math/cbc \ libccolamd.so:math/suitesparse-ccolamd \ libCgl.so:math/cgl \ libcholmod.so:math/suitesparse-cholmod \ libClp.so:math/clp \ libcminpack.so:math/cminpack \ libcoinasl.so:math/asl \ libCoinUtils.so:math/coinutils \ libcolamd.so:math/suitesparse-colamd \ libcxsparse.so:math/suitesparse-cxsparse \ libdlib.so:science/dlib-cpp \ libgif.so:graphics/giflib \ libgflags.so:devel/gflags \ libglog.so:devel/glog \ libgmp.so:math/gmp \ libhdf5_cpp.so:science/hdf5 \ libipopt.so:math/ipopt \ liblapack.so:math/lapack \ libmpc.so:math/mpc \ libmpfr.so:math/mpfr \ libnlopt.so:math/nlopt \ libOsi.so:math/osi \ libpagmo.so:science/pagmo2 \ libpng16.so:graphics/png \ libprimesieve.so:math/primesieve \ libspqr.so:math/suitesparse-spqr \ libsuitesparseconfig.so:math/suitesparse-config \ libsz.so:science/libaec \ libtbb.so:devel/onetbb USES= bison blaslapack:openblas cmake eigen:3 gnome jpeg localbase:ldflags pkgconfig sqlite xorg # compiler:c++17-lang USE_GITHUB= yes USE_GNOME= libxml2 USE_XORG= ice sm x11 xau xcb xdmcp xext USE_LDCONFIG= yes CMAKE_ARGS= -DBLAS_LIBRARIES=${LOCALBASE}/lib/libopenblas.so -DLAPACK_LIBRARIES=${LOCALBASE}/lib/libopenblas.so \ -DOPENTURNS_EXAMPLE_PATH:STRING=share/examples/openturns \ -DOPENTURNS_DOC_PATH:STRING=share/doc/openturns CMAKE_OFF= USE_DOXYGEN USE_SPHINX CMAKE_OFF+= USE_HMAT # broken with hmat-oss-1.7.1: https://github.com/openturns/openturns/issues/1868 CMAKE_OFF+= USE_CERES # ceres-solver-2.2.0 fails to be found by cmake, see https://github.com/ceres-solver/ceres-solver/issues/1023 TEST_TARGET= check # 10 tests are known to fail: https://github.com/openturns/openturns/issues/1919 OPTIONS_DEFINE= PYTHON EXAMPLES OPTIONS_DEFAULT= PYTHON OPTIONS_SUB= yes PYTHON_USES= python PYTHON_CMAKE_BOOL= BUILD_PYTHON PYTHON_CMAKE_ON= -DSWIG_EXECUTABLE=${LOCALBASE}/bin/swig PYTHON_PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}chaospy>0:math/py-chaospy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dill>0:devel/py-dill@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=1.3.1:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} PYTHON_BUILD_DEPENDS= swig:devel/swig \ ${PYTHON_PY_DEPENDS} PYTHON_RUN_DEPENDS= ${PYTHON_PY_DEPENDS} PORTEXAMPLES= * LLVM_VERSION= 12 # workaround for clang-13 crash: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=261341 # use clang from ports because cmake can't find base llvm for JIT BUILD_DEPENDS+= clang${LLVM_VERSION}:devel/llvm${LLVM_VERSION} RUN_DEPENDS+= clang${LLVM_VERSION}:devel/llvm${LLVM_VERSION} CPP= clang-cpp${LLVM_VERSION} CC= clang${LLVM_VERSION} CXX= clang++${LLVM_VERSION} post-install: @${RM} -r ${STAGEDIR}${DOCSDIR} .include diff --git a/math/py-cvxopt/Makefile b/math/py-cvxopt/Makefile index 154dfe3ded6c..31b441c7e6f8 100644 --- a/math/py-cvxopt/Makefile +++ b/math/py-cvxopt/Makefile @@ -1,60 +1,60 @@ PORTNAME= cvxopt DISTVERSION= 1.3.2 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python software for convex optimization WWW= https://github.com/cvxopt/cvxopt LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PY_SETUPTOOLS} \ ${PYTHON_PKGNAMEPREFIX}setuptools-scm>=6.2:devel/py-setuptools-scm@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libblas.so:math/blas \ libcholmod.so:math/suitesparse-cholmod \ libcolamd.so:math/suitesparse-colamd \ liblapack.so:math/lapack \ libsuitesparseconfig.so:math/suitesparse-config \ libumfpack.so:math/suitesparse-umfpack TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} USES= python localbase:ldflags cpe #USE_GITHUB= yes USE_PYTHON= pep517 autoplist CPE_VENDOR= cvxopt_project CFLAGS+= -I${LOCALBASE}/include/suitesparse OPTIONS_DEFINE= GSL FFTW GLPK DSDP OPTIONS_DEFAULT= GSL FFTW GLPK DSDP GSL_DESC= Build with GSL, the GNU scientific library GSL_MAKE_ENV= CVXOPT_BUILD_GSL=1 GSL_LIB_DEPENDS= libgsl.so:math/gsl FFTW_MAKE_ENV= CVXOPT_BUILD_FFTW=1 FFTW_LIB_DEPENDS= libfftw3.so:math/fftw3 GLPK_DESC= Build with GLPK, the linear programming solver GLPK_MAKE_ENV= CVXOPT_BUILD_GLPK=1 GLPK_LIB_DEPENDS= libglpk.so:math/glpk DSDP_DESC= Build with DSDP, the interior-point method DSDP_MAKE_ENV= CVXOPT_BUILD_DSDP=1 DSDP_CFLAGS= -I${LOCALBASE}/include/dsdp DSDP_LIB_DEPENDS= libdsdp.so:math/dsdp post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/cvxopt/*.so do-test: install @cd ${WRKSRC} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m pytest .include diff --git a/math/py-numpy/Makefile b/math/py-numpy/Makefile index 1c38114fc0b8..638e793f3a50 100644 --- a/math/py-numpy/Makefile +++ b/math/py-numpy/Makefile @@ -1,80 +1,80 @@ PORTNAME= numpy PORTVERSION= 1.25.0 -PORTREVISION= 6 +PORTREVISION= 7 PORTEPOCH= 1 CATEGORIES= math python MASTER_SITES= PYPI \ https://numpy.org/doc/1.23/:doc PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTFILES= ${DISTNAME}${EXTRACT_SUFX} \ ${PORTNAME}-ref.pdf:doc \ ${PORTNAME}-user.pdf:doc DIST_SUBDIR= ${PORTNAME}-${PORTVERSION:R} EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= python@FreeBSD.org COMMENT= The New Numeric Extension to Python WWW= https://www.numpy.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>=6.2.5:devel/py-pytest@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}hypothesis>=6.24.1:devel/py-hypothesis@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}typing-extensions>=4.2.0:devel/py-typing-extensions@${PY_FLAVOR} USES= compiler:c11 cpe fortran python:3.9-3.11 USE_PYTHON= allflavors autoplist concurrent cython distutils GCCLIBDIR_CMDS= ${FC} -print-file-name=libgfortran.so | ${SED} -e s/libgfortran.so// LDFLAGS+= -s PYDISTUTILS_BUILDARGS= --fcompiler=gnu95 PYDISTUTILS_CONFIGUREARGS= --fcompiler=gnu95 PORTDOCS= * OPTIONS_DEFINE= DOCS SUITESPARSE OPTIONS_SINGLE= BLASLIB OPTIONS_SINGLE_BLASLIB= ATLAS NETLIB OPENBLAS OPTIONS_DEFAULT= OPENBLAS SUITESPARSE SUITESPARSE_DESC= Use AMD and UMFPACK in SuiteSparse ATLAS_USES= blaslapack:atlas ATLAS_VARS= BLASLIBS="ptf77blas, ptcblas" BLASNAME=atlas LAPACKLIBS=alapack LIBRARIES=atlas_libs NETLIB_USES= blaslapack:netlib NETLIB_VARS= BLASLIBS="blas, cblas" BLASNAME=atlas LAPACKLIBS=lapack LIBRARIES=atlas_libs NETLIB_LIB_DEPENDS= libcblas.so:math/cblas OPENBLAS_USES= blaslapack:openblas OPENBLAS_VARS= BLASLIBS="openblas, gfortran" BLASNAME=openblas LAPACKLIBS="openblas, gfortran" LIBRARIES=libraries SUITESPARSE_LIB_DEPENDS=libumfpack.so:math/suitesparse-umfpack post-extract: @${TOUCH} ${WRKSRC}/numpy/f2py/tests/src/temp @${TOUCH} ${WRKSRC}/numpy/random/_examples/temp @${TOUCH} ${WRKSRC}/numpy/core/tests/examples/temp pre-configure-SUITESPARSE-off: @${REINPLACE_CMD} -e 's|:%%LOCALBASE%%/include/suitesparse||' ${WRKSRC}/site.cfg pre-configure: @${REINPLACE_CMD} -e 's|%%FC%%|${FC}|' ${WRKSRC}/numpy/distutils/fcompiler/gnu.py @${CP} ${FILESDIR}/site.cfg ${WRKSRC}/site.cfg ${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g' \ -e 's|%%BLASLIBS%%|${BLASLIBS}|; s|%%BLASNAME%%|${BLASNAME}|' \ -e 's|%%LAPACKLIBS%%|${LAPACKLIBS}|; s|%%LIBRARIES%%|${LIBRARIES}|' \ ${WRKSRC}/site.cfg @${REINPLACE_CMD} -e "s|%%GCCLIBDIR%%|$$(${GCCLIBDIR_CMDS})|" ${WRKSRC}/site.cfg ${WRKSRC}/numpy/distutils/system_info.py do-configure: post-install: ${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR} -name '*.so' | ${XARGS} ${STRIP_CMD} post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${_DISTDIR}/${PORTNAME}-ref.pdf ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${_DISTDIR}/${PORTNAME}-user.pdf ${STAGEDIR}${DOCSDIR} do-test: @cd ${WRKSRC} && ${PYTHON_CMD} runtests.py .include diff --git a/math/py-scikit-umfpack/Makefile b/math/py-scikit-umfpack/Makefile index 1a933428539f..d6fec626ce6a 100644 --- a/math/py-scikit-umfpack/Makefile +++ b/math/py-scikit-umfpack/Makefile @@ -1,33 +1,33 @@ PORTNAME= scikit-umfpack DISTVERSION= 0.3.3 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= math python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python interface to UMFPACK sparse direct solver WWW= https://scikit-umfpack.github.io/scikit-umfpack/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ swig:devel/swig LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libcblas.so:math/cblas \ libopenblas.so:math/openblas \ libumfpack.so:math/suitesparse-umfpack RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} USES= fortran python USE_PYTHON= distutils cython autoplist pytest # tests fail, see https://github.com/scikit-umfpack/scikit-umfpack/issues/77 TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/scikits/umfpack/__umfpack${PYTHON_EXT_SUFFIX}.so .include diff --git a/math/scilab/Makefile b/math/scilab/Makefile index 54896fe596fe..750a08a2ff41 100644 --- a/math/scilab/Makefile +++ b/math/scilab/Makefile @@ -1,191 +1,191 @@ PORTNAME= scilab PORTVERSION= 6.1.1 -PORTREVISION= 17 +PORTREVISION= 18 CATEGORIES= math cad java MASTER_SITES= https://www.scilab.org/download/${PORTVERSION}/ DISTFILES= ${DISTNAME}-src${EXTRACT_SUFX} MAINTAINER= ports@FreeBSD.org COMMENT= Scientific software package for numerical computations WWW= https://www.scilab.org LICENSE= GPLv2 BSD3CLAUSE LICENSE_COMB= dual LICENSE_FILE_GPLv2= ${WRKSRC}/COPYING LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/COPYING-BSD LIB_DEPENDS= libxml2.so:textproc/libxml2 \ libpcre.so:devel/pcre \ libcurl.so:ftp/curl \ libhdf5.so:science/hdf5 \ libarpack.so:math/arpack-ng \ libfftw3.so:math/fftw3 \ libmatio.so:math/matio \ libamd.so:math/suitesparse-amd \ libumfpack.so:math/suitesparse-umfpack RUN_DEPENDS= xdg-open:devel/xdg-utils USES= compiler:c++17-lang cpe desktop-file-utils eigen:3,build \ fortran gettext gmake gnome iconv:wchar_t libtool \ localbase ncurses pathfix pkgconfig shared-mime-info USE_LOCALE= en_US.UTF-8 GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-gfortran \ --without-emf \ --with-eigen-include=${LOCALBASE}/include/eigen3 \ ${ICONV_CONFIGURE_ARG} LDFLAGS+= ${ICONV_LIB} CONFIGURE_ENV= BLAS_LIBS="${BLASLIB}" LAPACK_LIBS="${LAPACKLIB}" INSTALL_TARGET= install-strip PLIST_SUB= SHLIB_VER=${PORTVERSION} OPTIONS_DEFINE= GUI OCAML TK OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= ATLAS NETLIB OPENBLAS OPTIONS_DEFAULT= GUI NETLIB OCAML TK OPTIONS_EXCLUDE_powerpc64= GUI OPTIONS_EXCLUDE_powerpc64le= GUI OPTIONS_SUB= yes ATLAS_USES= blaslapack:atlas NETLIB_USES= blaslapack:netlib OPENBLAS_USES= blaslapack:openblas GUI_DESC= Java-based Graphical User Interface OCAML_DESC= Scicos - dynamical system simulator (requires GUI) # Java dependencies: _GUI_DEPENDS+= ${JAVALIBDIR}/flexdock.jar:devel/flexdock \ ${JAVALIBDIR}/jogl2.jar:graphics/jogamp-jogl \ foprep:math/jeuclid \ ${JAVALIBDIR}/jhall.jar:java/javahelp \ ${JAVALIBDIR}/jrosetta-api.jar:java/jrosetta \ ${JAVALIBDIR}/commons-logging.jar:java/apache-commons-logging \ ${JAVALIBDIR}/jgraphx.jar:java/jgraphx \ ${JAVALIBDIR}/jlatexmath.jar:math/jlatexmath \ ${JAVALIBDIR}/ecj-4.4.2.jar:java/eclipse-ecj \ ${JAVALIBDIR}/lucene-core-5.5.5.jar:textproc/lucene5 # Documentation, graphic export: _GUI_DEPENDS+= ${LOCALBASE}/share/java/fop/build/fop.jar:textproc/fop \ ${JAVALIBDIR}/jlatexmath-fop.jar:math/jlatexmath \ ${LOCALBASE}/share/java/batik/lib/batik-all.jar:graphics/batik \ ${JAVALIBDIR}/avalon-framework.jar:devel/avalon-framework \ ${JAVALIBDIR}/commons-io.jar:devel/apache-commons-io \ ${JAVALIBDIR}/xmlgraphics-commons.jar:graphics/xmlgraphics-commons # Code quality: _GUI_DEPENDS+= ${JAVALIBDIR}/commons-beanutils.jar:java/apache-commons-beanutils \ ${JAVALIBDIR}/antlr.jar:devel/antlr \ ${JAVALIBDIR}/junit4.jar:java/junit \ ${LOCALBASE}/bin/splint:devel/splint # Documentation building: _GUI_DEPENDS+= ${LOCALBASE}/share/xsl/docbook/javahelp/javahelp.xsl:textproc/docbook-xsl \ ${JAVALIBDIR}/saxon-he-10.6.jar:textproc/saxon-he \ ${JAVALIBDIR}/xml-apis-ext.jar:textproc/xml-commons \ xsltproc:textproc/libxslt # Other gui deps: _GUI_DEPENDS+= ${JAVALIBDIR}/looks.jar:devel/jgoodies-looks \ ${JAVALIBDIR}/skinlf.jar:x11-toolkits/skinlf # Can't use USE_ANT because it overrides do-build target GUI_BUILD_DEPENDS= ${_GUI_DEPENDS} \ ant:devel/apache-ant GUI_RUN_DEPENDS= ${_GUI_DEPENDS} GUI_ALL_TARGET= all doc GUI_USES= gl GUI_USE= GL=gl JAVA=yes GUI_EXTRA_PATCHES= ${PATCHDIR}/extra-patch-bin-JAVA_HOME GUI_CONFIGURE_ON= --with-jdk=${JAVA_HOME} \ --with-docbook=${LOCALBASE}/share/xsl/docbook \ --enable-build-help GUI_CONFIGURE_OFF= --without-gui \ --without-javasci \ --without-xcos \ --disable-build-help OCAML_IMPLIES= GUI OCAML_CONFIGURE_WITH= modelica OCAML_BUILD_DEPENDS= ocaml:lang/ocaml \ ${LOCALBASE}/lib/ocaml/site-lib/num/META:math/ocaml-num OCAML_RUN_DEPENDS= ocaml:lang/ocaml TK_CONFIGURE_OFF= --without-tk TK_CONFIGURE_ON= --with-tk-library=${LOCALBASE}/lib \ --with-tk-include=${TK_INCLUDEDIR} \ --with-tcl-library=${LOCALBASE}/lib \ --with-tcl-include=${TCL_INCLUDEDIR} TK_USES= tk xorg TK_USE= XORG=x11 TK_RUN_DEPENDS= ${LOCALBASE}/lib/bwidget/init.tcl:x11-toolkits/bwidget .if !exists(/usr/include/omp.h) CONFIGURE_ARGS+= --without-openmp .endif .if defined(WITH_DEBUG) CONFIGURE_ARGS+= --enable-debug .endif .include .if ${COMPILER_TYPE} == clang && ${COMPILER_VERSION} >= 150 CFLAGS+= -Wno-error=int-conversion .endif .if ${COMPILER_TYPE} == clang && ${COMPILER_VERSION} >= 160 CFLAGS+= -Wno-error=incompatible-function-pointer-types .endif .if ${GCC_DEFAULT} >= 10 # workaround for Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar) FFLAGS+= -fallow-argument-mismatch .endif post-patch: @${REINPLACE_CMD} 's,/usr/local,${LOCALBASE},' ${WRKSRC}/etc/librarypath.xml @${REINPLACE_CMD} -e 's, gfortran, ${FC},' ${WRKSRC}/modules/dynamic_link/src/scripts/configure .if ${COMPILER_TYPE} == clang && ${COMPILER_VERSION} >= 160 @${REINPLACE_CMD} -e 's|std::filesystem|std::__fs::filesystem|g' \ ${WRKSRC}/modules/fileio/src/cpp/fullpath.cpp \ ${WRKSRC}/modules/fileio/sci_gateway/cpp/sci_get_absolute_file_path.cpp @${REINPLACE_CMD} -e 's|std::binary_function|std::__binary_function|' \ ${WRKSRC}/modules/ast/includes/types/sparseOp.hxx @${REINPLACE_CMD} -e 's|std::unary_function|std::__unary_function|' \ ${WRKSRC}/modules/ast/src/cpp/types/sparse.cpp .endif post-patch-GUI-on: # scilab segfaults on FreeBSD with C locale @${REINPLACE_CMD} 's,LC_ALL=C,,' ${WRKSRC}/Makefile.in @${REINPLACE_CMD} '/ac_java_jvm_jni_lib_flags/s,\(ljvm\),\1 -pthread,' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|/usr/lib/java|${JAVALIBDIR}|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|/usr/lib64/jni|${LOCALBASE}/lib/|g' ${WRKSRC}/configure @${REINPLACE_CMD} 's,\(DEFAULT_JAR_DIR="\),\1 \ ${LOCALBASE}/share/java/classes \ ${LOCALBASE}/share/java/fop/build \ ${LOCALBASE}/share/java/batik/lib \ ${LOCALBASE}/share/java/jeuclid/repo ,' ${WRKSRC}/configure # Prefer non-versioned files to avoid excessive rebuilds. This also fixes detection of fop. @${REINPLACE_CMD} 's|batik-all\*\.jar|batik-all.jar|g; \ s|commons-io\*\.jar|commons-io.jar|g; \ s|commons-logging\*\.jar|commons-logging.jar|g; \ s|fop\*\.jar|fop.jar|g; \ s|jlatexmath\*\.jar|jlatexmath.jar|g; \ s|xmlgraphics-commons\*\.jar|xmlgraphics-commons.jar|g' \ ${WRKSRC}/configure # Part of the jogamp-jogl-2.3 patch: @${REINPLACE_CMD} -e 's|javax.media.opengl.glu.GLUnurbs|com.jogamp.opengl.glu.GLUnurbs|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|jogamp.common.os.MachineDescriptionRuntime|jogamp.common.os.MachineDataInfoRuntime|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|%%JAVA_HOME%%|${JAVA_HOME}|' ${WRKSRC}/bin/scilab pre-install: ${MKDIR} ${STAGEDIR}${DATADIR}/.atoms post-install: @${FIND} ${STAGEDIR}${DATADIR}/modules -type d -empty -delete .include diff --git a/math/sundials/Makefile b/math/sundials/Makefile index 171b940af80b..bdbc2e9d80b9 100644 --- a/math/sundials/Makefile +++ b/math/sundials/Makefile @@ -1,81 +1,81 @@ PORTNAME= sundials DISTVERSION= 6.6.0 -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= math MASTER_SITES= https://github.com/LLNL/sundials/releases/download/v${DISTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers WWW= https://computing.llnl.gov/projects/sundials LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake:testing fortran localbase:ldflags python:build # 4 tests fail, see https://github.com/LLNL/sundials/issues/220 USE_LDCONFIG= yes CMAKE_ARGS= -DCMAKE_C_STANDARD=99 CMAKE_ON= ENABLE_PTHREAD CMAKE_OFF= BUILD_STATIC_LIBS \ EXAMPLES_ENABLE_C EXAMPLES_ENABLE_CXX EXAMPLES_ENABLE_F77 EXAMPLES_ENABLE_F90 CMAKE_TESTING_ON= SUNDIALS_TEST_UNITTESTS \ EXAMPLES_ENABLE_C EXAMPLES_ENABLE_CXX EXAMPLES_ENABLE_F77 EXAMPLES_ENABLE_F90 FCFLAGS:= ${FFLAGS} # project checks that these flags are equal OPTIONS_DEFINE= BLAS EXAMPLES KLU LAPACK MPI OPENMP OPTIONS_DEFAULT= KLU LAPACK MPI OPENMP OPTIONS_GROUP= VECTORS OPTIONS_GROUP_VECTORS= HYPRE PETSC VECTORS_DESC= Alternative vector libraries OPTIONS_SUB= yes BLAS_DESC= Enable BLAS support BLAS_CMAKE_BOOL= ENABLE_BLAS BLAS_USES= blaslapack:openblas #EXAMPLES_CMAKE_BOOL= EXAMPLES_ENABLE_C EXAMPLES_ENABLE_CXX EXAMPLES_ENABLE_F77 EXAMPLES_ENABLE_F90 #EXAMPLES_CMAKE_ON= -DEXAMPLES_INSTALL_PATH=${EXAMPLESDIR} #PORTEXAMPLES= * 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 # 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 HYPRE_BROKEN= ERROR: SUNDIALS interface to HYPRE is not functional. KLU_DESC= Use KLU package that is part of suitesparse KLU_CMAKE_BOOL= ENABLE_KLU KLU_CMAKE_ON= -DKLU_INCLUDE_DIR=${LOCALBASE}/include/suitesparse -DKLU_LIBRARY_DIR=${LOCALBASE}/lib KLU_LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libbtf.so:math/suitesparse-btf \ libcolamd.so:math/suitesparse-colamd \ libklu.so:math/suitesparse-klu \ libsuitesparseconfig.so:math/suitesparse-config LAPACK_DESC= Use Lapack linear algebra (sets SUNDIALS_INDEX_TYPE=int32) LAPACK_USES= blaslapack:openblas LAPACK_CMAKE_BOOL= ENABLE_LAPACK MPI_CMAKE_BOOL= ENABLE_MPI MPI_LIB_DEPENDS= libmpich.so:net/mpich OPENMP_CMAKE_BOOL= ENABLE_OPENMP 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=${LOCALBASE}/lib PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc PETSC_IMPLIES= MPI PETSC_PREVENTS= LAPACK # error: Incompatible sunindextype for LAPACK; disable LAPACK and rebuild PETSC_BROKEN= ERROR: PETSc not functional due to index size mismatch: SUNDIALS_INDEX_SIZE=64, but PETSc was built with 32-bit indices post-install: @${RM} ${STAGEDIR}${PREFIX}/include/sundials/LICENSE .include diff --git a/science/dynare/Makefile b/science/dynare/Makefile index aec9a20139b3..adc5d12ea3f3 100644 --- a/science/dynare/Makefile +++ b/science/dynare/Makefile @@ -1,56 +1,56 @@ PORTNAME= dynare DISTVERSION= 5.4 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= science # economics MASTER_SITES= https://www.dynare.org/release/source/ MAINTAINER= yuri@FreeBSD.org COMMENT= Software platform for handling a wide class of economic models WWW= https://www.dynare.org/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_aarch64= cannot open module file 'ieee_arithmetic.mod' for reading at (1): No such file or directory BUILD_DEPENDS= ${LOCALBASE}/include/boost/tokenizer.hpp:devel/boost-libs LIB_DEPENDS= libhdf5.so:science/hdf5 \ libmatio.so:math/matio \ libopenblas.so:math/openblas \ libsz.so:science/libaec RUN_DEPENDS= epstool:graphics/epstool \ gnuplot:math/gnuplot \ pstoedit:graphics/pstoedit \ xfig:graphics/xfig # README says that these executables are required for the test suite USES= bison compiler:c++17-lang fortran gmake localbase:ldflags tar:xz tex USE_TEX= pdftex GNU_CONFIGURE= yes CONFIGURE_ARGS= --disable-matlab \ --disable-doc FCFLAGS+= -fPIC # required because configure tests with -shared SUB_FILES= pkg-message OPTIONS_DEFINE= OCTAVE OPTIONS_DEFAULT= OCTAVE OPTIONS_SUB= yes OCTAVE_DESC= Integrate with Octave (main way to use Dynare) OCTAVE_CONFIGURE_ENABLE= octave OCTAVE_CONFIGURE_ON= --disable-mex-kalman-steady-state # Kalman Steady State MEX file for Octave - requires the non-free library slicot-5.0 OCTAVE_BUILD_DEPENDS= octave:math/octave OCTAVE_LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float \ libgsl.so:math/gsl \ libumfpack.so:math/suitesparse-umfpack OCTAVE_RUN_DEPENDS= octave:math/octave \ octave-forge-statistics>0:math/octave-forge-statistics post-install: # remove empty directories, see https://git.dynare.org/Dynare/dynare/-/issues/1835 @${FIND} ${STAGEDIR}${PREFIX} -type d -empty -delete .include diff --git a/science/mbdyn/Makefile b/science/mbdyn/Makefile index a601b39b80e0..6948babf6a4d 100644 --- a/science/mbdyn/Makefile +++ b/science/mbdyn/Makefile @@ -1,72 +1,72 @@ PORTNAME= mbdyn DISTVERSION= 1.7.3 -PORTREVISION= 15 +PORTREVISION= 16 CATEGORIES= science MASTER_SITES= https://www.mbdyn.org/userfiles/downloads/ MAINTAINER= yuri@FreeBSD.org COMMENT= MultiBody Dynamics analysis system WWW= https://www.mbdyn.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_powerpc= does not compile on powerpc BUILD_DEPENDS= libatomic_ops>0:devel/libatomic_ops LIB_DEPENDS= libltdl.so:devel/libltdl \ libarpack.so:math/arpack-ng \ libumfpack.so:math/suitesparse-umfpack USES= compiler:c++11-lib fortran gmake libtool:build localbase USE_LDCONFIG= yes USE_CXXSTD= c++14 # fix build breakage with clang16 due to use of deprecated feature 'dynamic exception specifications', see https://public.gitlab.polimi.it/DAER/mbdyn/-/issues/339 CPPFLAGS+= -fpermissive -I${LOCALBASE}/include/suitesparse GNU_CONFIGURE= yes GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share CONFIGURE_ARGS= --program-prefix='' --enable-multithread --with-mpi=no \ --with-ginac=no INSTALL_TARGET= install-strip OPTIONS_DEFINE= METIS CHACO OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= REFERENCE ATLAS OPTIONS_DEFAULT= REFERENCE ATLAS_DESC= ATLAS CHACO_DESC= Enable chaco-support METIS_DESC= Enable metis-support REFERENCE_DESC= Blas / Lapack ATLAS_CONFIGURE_ON= --with-blas=atlas ATLAS_USES= blaslapack:atlas CHACO_BUILD_DEPENDS= ${LOCALBASE}/lib/libchaco.a:math/chaco CHACO_CONFIGURE_ON= --with-chaco=yes CHACO_CONFIGURE_OFF= --with-chaco=no METIS_CONFIGURE_ON= --with-metis=yes METIS_CONFIGURE_OFF= --with-metis=no METIS_CPPFLAGS= -I${LOCALBASE}/include/metis METIS_LIB_DEPENDS= libmetis.so:math/metis REFERENCE_CONFIGURE_ON= --with-blas=blas REFERENCE_USES= blaslapack:netlib .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch in argument 't' at (1); passed REAL(4) to INTEGER(4) # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif pre-configure: ${REINPLACE_CMD} -e '/try_lapack_LIBS=/s/-llapack/${LAPACKLIB}/' \ -e 's/ -lxerbla//; s/-lcholmod/-lcholmod ${BLASLIB} ${LAPACKLIB} -lsuitesparseconfig/' \ ${WRKSRC}/configure .include diff --git a/science/py-scikit-sparse/Makefile b/science/py-scikit-sparse/Makefile index 1143b32f5ece..f04fc9abc1e7 100644 --- a/science/py-scikit-sparse/Makefile +++ b/science/py-scikit-sparse/Makefile @@ -1,30 +1,30 @@ PORTNAME= scikit-sparse DISTVERSION= 0.4.8 -PORTREVISION= 8 +PORTREVISION= 9 CATEGORIES= science python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Sparse matrix package WWW= https://github.com/scikit-sparse/scikit-sparse LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= ${RUN_DEPENDS} LIB_DEPENDS= libumfpack.so:math/suitesparse-umfpack \ libcholmod.so:math/suitesparse-cholmod RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} USES= fortran python USE_PYTHON= distutils cython autoplist CFLAGS+= -I${LOCALBASE}/include/suitesparse LDFLAGS+= -shared post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/sksparse/cholmod*.so .include diff --git a/science/siconos/Makefile b/science/siconos/Makefile index b98ee4ea1671..3eeefb2cf527 100644 --- a/science/siconos/Makefile +++ b/science/siconos/Makefile @@ -1,49 +1,49 @@ PORTNAME= siconos DISTVERSION= 4.4.0 -PORTREVISION= 11 +PORTREVISION= 12 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Simulation framework for nonsmooth dynamical systems WWW= https://nonsmooth.gricad-pages.univ-grenoble-alpes.fr/siconos/index.html LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_i386= non-constant-expression cannot be narrowed from type 'unsigned int' to 'npy_intp', see https://github.com/siconos/siconos/issues/416 BUILD_DEPENDS= boost-libs>0:devel/boost-libs \ ${PYTHON_PKGNAMEPREFIX}packaging>0:devel/py-packaging@${PY_FLAVOR} \ help2man:misc/help2man LIB_DEPENDS= libcxsparse.so:math/suitesparse-cxsparse \ libgmp.so:math/gmp \ libldl.so:math/suitesparse-ldl \ libopenblas.so:math/openblas TEST_DEPENDS= cppunit>0:devel/cppunit USES= cmake:testing compiler:c++17-lang fortran pkgconfig USE_GITHUB= yes USE_LDCONFIG= yes CMAKE_ARGS= -DFREEBSD_PYTHON_VER=${PYTHON_VER} CMAKE_TESTING_ON= WITH_TESTING # tests are broken, see https://github.com/siconos/siconos/issues/415 CFLAGS+= -DCLOCKTIME -DCLOCKS_PER_SEC=128 # workaround for 'Undefined symbol "ftime"', see https://github.com/siconos/siconos/issues/411 BINARY_ALIAS= python3=${PYTHON_CMD} OPTIONS_DEFINE= PYTHON OPTIONS_DEFAULT= #PYTHON OPTIONS_SUB= yes PYTHON_CMAKE_BOOL= WITH_PYTHON_WRAPPER PYTHON_USES= python PYTHON_USES_OFF= python:build PYTHON_PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} PYTHON_BUILD_DEPENDS= ${PYTHON_PY_DEPENDS} \ swig:devel/swig PYTHON_RUN_DEPENDS= ${PYTHON_PY_DEPENDS} PYTHON_BROKEN= Fails to import, see https://github.com/siconos/siconos/issues/420 .include diff --git a/science/trilinos/Makefile b/science/trilinos/Makefile index 8a11a7d2bd86..44f10e85d9b2 100644 --- a/science/trilinos/Makefile +++ b/science/trilinos/Makefile @@ -1,86 +1,87 @@ PORTNAME= trilinos DISTVERSIONPREFIX= trilinos-release- DISTVERSION= 15-1-1 +PORTREVISION= 1 CATEGORIES= science # physics MAINTAINER= yuri@FreeBSD.org COMMENT= Solver for multi-physics engineering and scientific problems WWW= https://trilinos.github.io/ LICENSE= BSD3CLAUSE LGPL20 # Trilinos is licensed on a per-package basis. Most packages are under a BSD license, some are published under the (L)GPL. LICENSE_COMB= multi BROKEN_armv6= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte BROKEN_armv7= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte BROKEN_i386= kokkos assumes a 64-bit build; i.e., 8-byte pointers, but found 4-byte BUILD_DEPENDS= bash:shells/bash \ boost-libs>0:devel/boost-libs \ swig:devel/swig \ ${PYNUMPY} LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libblas.so:math/blas \ liblapack.so:math/lapack \ libumfpack.so:math/suitesparse-umfpack RUN_DEPENDS= bash:shells/bash USES= cmake compiler:c++14-lang fortran perl5 python shebangfix USE_LDCONFIG= yes USE_GITHUB= yes GH_PROJECT= Trilinos SHEBANG_FILES= packages/kokkos/bin/kokkos_launch_compiler \ packages/kokkos/bin/nvcc_wrapper \ packages/phalanx/scripts/phalanx_create_evaluator.py CXXFLAGS+= -DBOOST_STACKTRACE_GNU_SOURCE_NOT_REQUIRED # fails otherwise with backtrace-related symbol error explicitly printed by Boost LDFLAGS+= -lexecinfo # only for kokkos (?), to prevent missing symbols CONFLICTS= kokkos # installs bundled kokkos, need to figure out how to prevent this CONFLICTS_INSTALL= googletest # see https://github.com/trilinos/Trilinos/issues/11271 ## configure Trilinos # general #CMAKE_ARGS+= -DTrilinos_VERBOSE_CONFIGURE=ON CMAKE_ARGS+= -DCMAKE_INSTALL_PREFIX:PATH=${PREFIX} CMAKE_ARGS+= -DBUILD_SHARED_LIBS:BOOL=ON # package selection CMAKE_ARGS+= -DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON CMAKE_ARGS+= -DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON CMAKE_ARGS+= -DTrilinos_ENABLE_SEACAS:BOOL=OFF # because of pumagon, etc failure (need to retest) CMAKE_ARGS+= -DTrilinos_ENABLE_PyTrilinos:BOOL=OFF # workaround for https://github.com/trilinos/Trilinos/issues/12184 # parallelism-related CMAKE_ARGS+= -DTrilinos_ENABLE_OpenMP:BOOL=OFF #CMAKE_ARGS+= -DKokkos_ENABLE_Pthread:BOOL=ON #CMAKE_ARGS+= -DTPL_ENABLE_Pthread:BOOL=ON #CMAKE_ARGS+= -DTPL_ENABLE_MPI:BOOL=ON #CMAKE_ARGS+= -DMPI_BASE_DIR:PATH="${LOCALBASE}/mpi/openmpi" #CMAKE_ARGS+= -DMPI_BIN_DIR:PATH="${LOCALBASE}/mpi/openmpi/bin" ## additional features/packages required by Xyce CMAKE_ON+= EpetraExt_BUILD_BTF CMAKE_ON+= EpetraExt_BUILD_EXPERIMENTAL CMAKE_ON+= EpetraExt_BUILD_GRAPH_REORDERINGS #CMAKE_ON+= Teuchos_ENABLE_COMPLEX # this feature is broken in Trilinos CMAKE_ON+= Trilinos_ENABLE_COMPLEX_DOUBLE # Enabling the UMFPACK feature required by the above features. CMAKE_ON+= TPL_ENABLE_UMFPACK CMAKE_ON+= TPL_ENABLE_AMD CMAKE_ARGS+= -DUMFPACK_INCLUDE_DIRS=${LOCALBASE}/include/suitesparse CMAKE_ARGS+= -DTPL_AMD_INCLUDE_DIRS=${LOCALBASE}/include/suitesparse CMAKE_ARGS+= -DAMD_LIBRARY_DIRS=${LOCALBASE}/lib # users: https://duongdo27.github.io/Trilinos/users.html CONFLICTS_INSTALL= googletest # installs files into the same place, problematic file: /usr/local/include/gtest/gtest.h, see https://github.com/trilinos/Trilinos/issues/11184 post-install: # remove MPI headers that it installs @${RM} ${STAGEDIR}${PREFIX}/include/mpi*.h .include