diff --git a/astro/oskar/Makefile b/astro/oskar/Makefile index a3b2bd69c1b8..f34faf9bc5a2 100644 --- a/astro/oskar/Makefile +++ b/astro/oskar/Makefile @@ -1,30 +1,31 @@ PORTNAME= OSKAR DISTVERSION= 2.8.3 +PORTREVISION= 1 CATEGORIES= astro MAINTAINER= yuri@FreeBSD.org COMMENT= SKA Radio telescope simulator LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE ONLY_FOR_ARCHS= amd64 i386 powerpc powerpc64 powerpc64le ONLY_FOR_ARCHS_REASON= gccfeatures.h:54:4: This code has only been tested on x86 and powerpc platforms BROKEN_FreeBSD_12_powerpc64= fails to compile: oskar_convert_cirs_relative_directions_to_enu_directions.c:67:29: 'csinl' undeclared (first use in this function) LIB_DEPENDS= libcfitsio.so:astro/cfitsio \ libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake compiler:c++11-lang localbase:ldflags python qt:5 \ shebangfix USE_QT= core gui network widgets buildtools_build qmake_build USE_LDCONFIG= yes SHEBANG_FILES= apps/oskar_convert_cst_to_scalar.py USE_GITHUB= yes GH_ACCOUNT= OxfordSKA CMAKE_ARGS= -DFREEBSD_FILESDIR:STRING=${FILESDIR} .include diff --git a/audio/csound/Makefile b/audio/csound/Makefile index d4770a67ff9d..4943b200d680 100644 --- a/audio/csound/Makefile +++ b/audio/csound/Makefile @@ -1,196 +1,196 @@ # Created by: trevor PORTNAME= csound DISTVERSION= 6.15.0 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= audio lang MAINTAINER= yuri@FreeBSD.org COMMENT= Sound synthesizer LICENSE= LGPL21+ LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= boost-libs>0:devel/boost-libs \ swig:devel/swig \ gmm++>0:math/gmm++ LIB_DEPENDS= libsamplerate.so:audio/libsamplerate \ libsndfile.so:audio/libsndfile USES= alias bison cmake compiler:c++11-lib cpe eigen:3 localbase ncurses python:build # is python needed: https://github.com/csound/csound/issues/1437 ? USE_GITHUB= yes USE_LDCONFIG= yes CPE_VENDOR= csounds CONFLICTS_INSTALL= clearsilver go-cs libextractor outguess CFLAGS_powerpc= -maltivec CFLAGS_powerpcspe= -DPFFFT_SIMD_DISABLE CMAKE_ARGS= -DBUILD_CSOUNDVST:BOOL=OFF \ -DBUILD_PD_CLASS:BOOL=OFF \ -DPYTHON_MODULE_INSTALL_DIR:PATH="${PYTHONPREFIX_SITELIBDIR}" \ -DOPSYS:STRING="${OPSYS}" CMAKE_OFF= USE_ALSA BUILD_JAVA_INTERFACE BUILD_TESTS SSP_UNSAFE= yes LDFLAGS+= -lexecinfo SUB_FILES= pkg-message OPTIONS_DEFINE= CURL FLTK HDF5 NLS OPENMP PORTAUDIO PULSEAUDIO OPTIONS_GROUP= OPCODES # list is in Opcodes/CMakeLists.txt OPTIONS_GROUP_OPCODES= BUCHLA CHUA COUNTER DSSI EXCITER FAUST FLUIDSYNTH IMAGE JACK LUA LINALG MP3OUT OSC P5GLOVE PADSYNTH PLATEREV PVSGENDY PYTHON SCANSYN SELECT SERIAL STACK STK VST4CS WIIMOTE # Opcodes/CMakeLists.txt, Opcodes/stk/CMakeLists.txt OPTIONS_DEFAULT= FLTK OPENMP OPTIONS_DEFAULT+= BUCHLA CHUA DSSI EXCITER FAUST IMAGE JACK LINALG OSC P5GLOVE PADSYNTH PLATEREV SCANSYN SELECT SERIAL STACK STK # for OPCODES OPTIONS_SUB= yes OPCODES_DESC= Build/install opcodes BUCHLA_DESC= Build the Buchla filter opcode BUCHLA_CMAKE_BOOL= BUILD_BUCHLA_OPCODES CHUA_DESC= Build the chua opcodes CHUA_CMAKE_BOOL= BUILD_CHUA_OPCODES COUNTER_DESC= Build the serial opcode COUNTER_CMAKE_BOOL= BUILD_COUNTER_OPCODES CURL_CMAKE_BOOL= USE_CURL # see https://github.com/csound/csound/issues/1067 CURL_LIB_DEPENDS= libcurl.so:ftp/curl DSSI_DESC= Build DSSI opcodes DSSI_BUILD_DEPENDS= dssi>0:audio/dssi DSSI_LIB_DEPENDS= libdssialsacompat.so:audio/libdssialsacompat DSSI_RUN_DEPENDS= dssi>0:audio/dssi DSSI_CMAKE_BOOL= BUILD_DSSI_OPCODES DSSI_CFLAGS= -isystem ${LOCALBASE}/include/dssi EXCITER_DESC= Build the exciter opcode EXCITER_CMAKE_BOOL= BUILD_EXCITER_OPCODES FLTK_DESC= Build FLTK plugin and GUI FLTK_USES= xorg FLTK_USE= XORG=ice,sm,x11,xext FLTK_LIB_DEPENDS= libfltk.so:x11-toolkits/fltk FLTK_CMAKE_ON= -DBUILD_WINSOUND:BOOL=ON FLTK_CMAKE_OFF= -DBUILD_CSOUND_AC:BOOL=OFF \ -DBUILD_VIRTUAL_KEYBOARD:BOOL=OFF \ -DUSE_FLTK:BOOL=OFF FAUST_DESC= Build the Faust opcodes FAUST_USES= ssl FAUST_LLVM_VERSION= 11 # should be the same as in audio/faust FAUST_LIB_DEPENDS= libfaust.so:audio/faust FAUST_CMAKE_BOOL= BUILD_FAUST_OPCODES FAUST_CMAKE_ON= -DFAUST_LLVM_VERSION:STRING=${FAUST_LLVM_VERSION} FLUIDSYNTH_DESC= Building FluidSynth opcodes FLUIDSYNTH_LIB_DEPENDS= libfluidsynth.so:audio/fluidsynth FLUIDSYNTH_CMAKE_BOOL= BUILD_FLUID_OPCODES FLUIDSYNTH_BROKEN= FluidSynth 2.x is broken upstream: https://github.com/csound/csound/issues/1078#issuecomment-441459803 HDF5_DESC= Build HDF5 read/write plugin HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec HDF5_CMAKE_BOOL= BUILD_HDF5_OPCODES JACK_DESC= Build the JACK related opcodes JACK_LIB_DEPENDS= libjack.so:audio/jack JACK_CMAKE_BOOL= BUILD_JACK_OPCODES USE_JACK LINALG_DESC= Build the linear algebra opcodes LINALG_CMAKE_BOOL= BUILD_LINEAR_ALGEBRA_OPCODES LINALG_CXXFLAGS= -DGMM_VERSION=x # workaround based on https://github.com/csound/csound/issues/1069#issuecomment-439648756 LUA_DESC= Build Lua Interface and module LUA_LIB_DEPENDS= libluajit-5.1.so:lang/luajit LUA_CMAKE_BOOL= BUILD_CSOUND_AC_LUA_INTERFACE BUILD_LUA_INTERFACE BUILD_LUA_OPCODES NLS_USES= gettext NLS_CMAKE_OFF= -DGETTEXT_MSGFMT_EXECUTABLE:FILEPATH="" \ -DGETTEXT_MSGMERGE_EXECUTABLE:FILEPATH="" \ -DLIBINTL_LIBRARY:FILEPATH="" \ -DUSE_GETTEXT:BOOL=OFF OPENMP_CMAKE_BOOL= USE_OPEN_MP MP3OUT_DESC= Build MP3OUT opcodes MP3OUT_CMAKE_BOOL= BUILD_MP3OUT_OPCODE OSC_DESC= Build OSC opcodes OSC_LIB_DEPENDS= liblo.so:audio/liblo OSC_CMAKE_BOOL= BUILD_OSC_OPCODES PADSYNTH_DESC= Build the Padsynth opcode PADSYNTH_CMAKE_BOOL= BUILD_PADSYNTH_OPCODES IMAGE_DESC= Build Image opcodes IMAGE_LIB_DEPENDS= libpng.so:graphics/png IMAGE_CMAKE_BOOL= BUILD_IMAGE_OPCODES P5GLOVE_DESC= Build PortAudio I/O module P5GLOVE_CMAKE_BOOL= BUILD_P5GLOVE_OPCODES PORTAUDIO_DESC= Build PortAudio I/O module PORTAUDIO_LIB_DEPENDS= libportaudio.so:audio/portaudio PORTAUDIO_CMAKE_BOOL= USE_PORTAUDIO PULSEAUDIO_DESC= Build PulseAudio I/O module PULSEAUDIO_LIB_DEPENDS= libpulse-simple.so:audio/pulseaudio PULSEAUDIO_CMAKE_BOOL= USE_PULSEAUDIO PLATEREV_DESC= Build the platerev opcode PLATEREV_CMAKE_BOOL= BUILD_PLATEREV_OPCODES PVSGENDY_DESC= Build the pvsgendy opcode PVSGENDY_CMAKE_BOOL= BUILD_PVSGENDY_OPCODE PYTHON_DESC= Build the Python opcodes PYTHON_USES= python PYTHON_CMAKE_BOOL= BUILD_PYTHON_OPCODES SCANSYN_DESC= Build the select opcodes SCANSYN_CMAKE_BOOL= BUILD_SCANSYN_OPCODES SELECT_DESC= Build the select opcode SELECT_CMAKE_BOOL= BUILD_SELECT_OPCODE SERIAL_DESC= Build the serial opcode SERIAL_CMAKE_BOOL= BUILD_SERIAL_OPCODES STACK_DESC= Build the stack opcodes STACK_CMAKE_BOOL= BUILD_STACK_OPCODES STK_DESC= Build the stk opcodes STK_CMAKE_BOOL= BUILD_STK_OPCODES STK_LIB_DEPENDS= libstk.so:audio/stk VST4CS_DESC= Build the vst4cs opcodes VST4CS_CMAKE_BOOL= BUILD_VST4CS_OPCODES WIIMOTE_DESC= Build the Wiimote opcodes WIIMOTE_CMAKE_BOOL= BUILD_WIIMOTE_OPCODES WIIMOTE_BROKEN= Need to port wiiuse: https://github.com/rpavlik/wiiuse post-patch: @${REINPLACE_CMD} -e \ 's|/usr/include/Python2.7|${PYTHON_INCLUDEDIR}| ; \ s|/usr/local|${LOCALBASE}| ; \ /linuxjoystick/s|^|#| ; \ s| dl)|)|' \ ${WRKSRC}/Opcodes/CMakeLists.txt @${REINPLACE_CMD} -e \ '/CMAKE_SYSTEM_NAME/s|"Linux"|"${OPSYS}"|' \ ${WRKSRC}/Frontends/CMakeLists.txt @${REINPLACE_CMD} -e \ 's| mixer)| csmixer)|' \ ${WRKSRC}/util/CMakeLists.txt post-install: @${LN} -sf libcsnd6.so.6.0 ${STAGEDIR}${PREFIX}/lib/libcsnd6.so.6 @${LN} -sf libcsound64.so.6.0 ${STAGEDIR}${PREFIX}/lib/libcsound64.so.6 post-install-FLTK-on: @${LN} -sf libCsoundAC.so.6.0 ${STAGEDIR}${PREFIX}/lib/libCsoundAC.so.6 .include diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 3d4aecd0b9d3..d28827b7ee2a 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -1,44 +1,45 @@ PORTNAME= kallisto DISTVERSIONPREFIX= v DISTVERSION= 0.48.0 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Quantify abundances of transcripts from RNA-Seq data LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt BUILD_DEPENDS= autoconf>=0:devel/autoconf LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libhts.so:biology/htslib USES= cmake:noninja compiler:c++11-lang gmake localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= pachterlab SUB_FILES= kallisto-test PORTEXAMPLES= * PLIST_FILES= bin/kallisto EXAMPLES_PLIST_FILES= bin/kallisto-test # hdf5 is being phased out and is no longer built in by default, but is still # required for Sleuth (requires kallisto bootstrap estimates) and other # downstream tools. Remove this after Sleuth et al catch up. CMAKE_ARGS+= -DUSE_HDF5:BOOL=ON MAKE_JOBS_UNSAFE= yes LDFLAGS+= -lhts -lz OPTIONS_DEFINE= EXAMPLES post-extract: ${RM} -rf ${WRKSRC}/ext/htslib post-install-EXAMPLES-on: ${INSTALL_SCRIPT} ${WRKDIR}/kallisto-test ${STAGEDIR}${PREFIX}/bin cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/cad/appcsxcad/Makefile b/cad/appcsxcad/Makefile index bd3f82a76564..221694424c61 100644 --- a/cad/appcsxcad/Makefile +++ b/cad/appcsxcad/Makefile @@ -1,42 +1,43 @@ PORTNAME= appcsxcad DISTVERSIONPREFIX= v DISTVERSION= 0.2.2-7 +PORTREVISION= 1 DISTVERSIONSUFFIX= -gde8c271 CATEGORIES= cad MAINTAINER= yuri@FreeBSD.org COMMENT= Minimal GUI Application using the QCSXCAD library LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING # many dependencies below are induced by vtk8, but not vtk9 LIB_DEPENDS= \ libCSXCAD.so:cad/csxcad \ libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libhdf5.so:science/hdf5 \ libpng16.so:graphics/png \ libQCSXCAD.so:cad/qcsxcad \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libtiff.so:graphics/tiff \ libvtkCommonCore-8.2.so:math/vtk8 # some related packages don't support vtk9 yet, see https://github.com/thliebig/QCSXCAD/issues/6#issuecomment-901633240 USES= cmake jpeg pkgconfig qt:5 xorg USE_QT= core gui sql widgets xml buildtools_build qmake_build USE_XORG= ice sm x11 xext xt USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= thliebig GH_PROJECT= AppCSXCAD CMAKE_ARGS= -DVTK_DIR=${LOCALBASE}/lib/vtk-8.2/cmake/vtk-8.2 PLIST_FILES= bin/AppCSXCAD \ bin/AppCSXCAD.sh post-install: @${REINPLACE_CMD} -i '' -e 's|#!/bin/bash|#!/bin/sh|' ${STAGEDIR}${PREFIX}/bin/AppCSXCAD.sh .include diff --git a/cad/csxcad/Makefile b/cad/csxcad/Makefile index debd9eb8558d..a7ddeae89644 100644 --- a/cad/csxcad/Makefile +++ b/cad/csxcad/Makefile @@ -1,37 +1,37 @@ PORTNAME= csxcad DISTVERSIONPREFIX= v DISTVERSION= 0.6.2-103 DISTVERSIONSUFFIX= -g3c4fb66 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= cad MAINTAINER= yuri@FreeBSD.org COMMENT= C++ library to describe geometrical objects LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= cgal>0:math/cgal # many dependencies below are induced by vtk8, but not vtk9 LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libfparser-4.5.so:math/fparser \ libgmp.so:math/gmp \ libhdf5.so:science/hdf5 \ libmpfr.so:math/mpfr \ libpng16.so:graphics/png \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libtiff.so:graphics/tiff \ libtinyxml.so:textproc/tinyxml \ libvtkCommonCore-8.2.so:math/vtk8 # some related packages don't support vtk9 yet, see https://github.com/thliebig/QCSXCAD/issues/6#issuecomment-901633240 USES= cmake jpeg pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= thliebig GH_PROJECT= ${PORTNAME:tu} CMAKE_ARGS= -DFPARSER_ROOT_DIR=${LOCALBASE} \ -DVTK_DIR=${LOCALBASE}/lib/vtk-8.2/cmake/vtk-8.2 .include diff --git a/cad/gmsh/Makefile b/cad/gmsh/Makefile index d1265eb03ca4..2370e67e0376 100644 --- a/cad/gmsh/Makefile +++ b/cad/gmsh/Makefile @@ -1,69 +1,70 @@ # Created by: Pedro Giffuni PORTNAME= gmsh DISTVERSION= 4.9.2 +PORTREVISION= 1 CATEGORIES= cad MASTER_SITES= http://gmsh.info/src/ DISTNAME= ${PORTNAME}-${PORTVERSION}-source DIST_SUBDIR= gmsh MAINTAINER= wen@FreeBSD.org COMMENT= Automatic 3D finite element mesh generator LICENSE= AGPLv3+ APACHE20 GPLv3+ GPLv2+ LGPL21 LICENSE_COMB= multi LIB_DEPENDS= libfltk.so:x11-toolkits/fltk \ libfontconfig.so:x11-fonts/fontconfig \ libgmp.so:math/gmp \ libhdf5.so:science/hdf5 \ libpng.so:graphics/png \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libfreetype.so:print/freetype2 RUN_DEPENDS= getdp:science/getdp USES= blaslapack compiler:c++11-lang cmake fortran gl jpeg tar:tgz \ xorg USE_GL= gl glu USE_XORG= x11 xcursor xext xinerama xfixes xft xrender CMAKE_ARGS= -DCMAKE_SKIP_RPATH:BOOL=YES LDFLAGS+= -lexecinfo OPTIONS_DEFINE= CGNS DOCS MED OCC SHARED STATIC OPTIONS_DEFAULT= CGNS MED OCC OPTIONS_SUB= yes CGNS_DESC= Enable CGNS mesh import MED_DESC= Enable MED mesh and post file formats OCC_DESC= Enable OpenCASCADE geometrical models SHARED_DESC= Build shared library and install header files STATIC_DESC= Build static library PLIST_SUB= VER=${PORTVERSION} VE=${PORTVERSION:R} # TODO # Dependencies against PythonLibs, swig and petsc are found and registered if # installed # => add knobs to handle them. CGNS_CMAKE_BOOL= ENABLE_CGNS CGNS_LIB_DEPENDS= libcgns.so:science/cgnslib DOCS_CMAKE_BOOL= INSTALL_DOCS MED_CMAKE_BOOL= ENABLE_MED MED_LIB_DEPENDS= libmed.so:french/med OCC_CMAKE_BOOL= ENABLE_OCC OCC_CMAKE_ON= -DOCC_INC=${LOCALBASE}/include/OpenCASCADE OCC_LIB_DEPENDS= libopenblas.so:math/openblas libTKernel.so:cad/opencascade OCC_USES= gnome OCC_USE= gnome=cairo SHARED_CMAKE_BOOL= ENABLE_BUILD_SHARED SHARED_USE= LDCONFIG=yes STATIC_CMAKE_BOOL= ENABLE_BUILD_LIB post-install-SHARED-on: ${RM} -r ${STAGEDIR}/wrkdirs .include diff --git a/graphics/alembic/Makefile b/graphics/alembic/Makefile index 95de2628970b..cd15e5bf8f69 100644 --- a/graphics/alembic/Makefile +++ b/graphics/alembic/Makefile @@ -1,33 +1,34 @@ # Created by: Alexey Dokuchaev PORTNAME= alembic PORTVERSION= 1.8.3 +PORTREVISION= 1 CATEGORIES= graphics MAINTAINER= danfe@FreeBSD.org COMMENT= Open framework for storing and sharing graphic scene data LICENSE= BSD3CLAUSE LIB_DEPENDS= libImath.so:math/Imath -LIB_DEPENDS+= libsz.so:science/szip +LIB_DEPENDS+= libsz.so:science/libaec USES= cmake compiler:c++11-lang USE_CXXSTD= c++11 USE_GITHUB= yes USE_LDCONFIG= yes OPTIONS_DEFINE= HDF5 OPTIONS_DEFAULT= HDF5 OPTIONS_SUB= yes HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_CMAKE_ON= -DUSE_HDF5:BOOL=ON PLIST_FILES= lib/libAlembic.so.${PORTVERSION} \ lib/libAlembic.so.${PORTVERSION:R} do-test: @cd ${TEST_WRKSRC} && ctest -C ${CMAKE_BUILD_TYPE} ${_MAKE_JOBS} .include diff --git a/graphics/qgis-ltr/Makefile b/graphics/qgis-ltr/Makefile index e6c10ac207c7..74e795553ccf 100644 --- a/graphics/qgis-ltr/Makefile +++ b/graphics/qgis-ltr/Makefile @@ -1,183 +1,184 @@ # Created by: Laurent Courty PORTNAME= qgis DISTVERSION= 3.22.7 +PORTREVISION= 1 CATEGORIES= graphics geography MASTER_SITES= https://qgis.org/downloads/ PKGNAMESUFFIX= -ltr MAINTAINER= rhurlin@FreeBSD.org COMMENT= Free and Open Source Geographic Information System LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/doc/LICENSE BUILD_DEPENDS= gpsbabel>=1.5.4:astro/gpsbabel \ opencl>=0:devel/opencl \ ${PYTHON_PKGNAMEPREFIX}cycler>=0.10.0:devel/py-cycler@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dateutil>=2.8.1:devel/py-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>=0.18.2:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}httplib2>=0.17.3:www/py-httplib2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=2.10.1:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}markupsafe>=1.1.1:textproc/py-markupsafe@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.4:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>=3.0.5:devel/py-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0.24.1:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pbr>=3.1.1:devel/py-pbr@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pip>=19.1.1:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plotly>=3.0.2:graphics/py-plotly@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygments>=2.5.2:textproc/py-pygments@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyproj>=2.1.3:graphics/py-pyproj@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytz>=2020.1:devel/py-pytz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.22.0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>=1.14.0:devel/py-six@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlite3>=3.7.7:databases/py-sqlite3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=5.3.1:devel/py-yaml@${PY_FLAVOR} LIB_DEPENDS= libexiv2.so:graphics/exiv2 \ libexpat.so:textproc/expat2 \ libgdal.so:graphics/gdal \ libgeos.so:graphics/geos \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ liblazperf.so:archivers/lazperf \ libmdal.so:math/mdal \ libnetcdf.so:science/netcdf \ libOpenCL.so:devel/ocl-icd \ libpdal_base.so:math/pdal \ libproj.so:graphics/proj \ libprotobuf-lite.so:devel/protobuf \ libqjson-qt5.so:devel/qjson \ libqscintilla2_qt5.so:devel/qscintilla2-qt5 \ libqt5keychain.so:security/qtkeychain \ libqwt6.so:x11-toolkits/qwt6 \ libspatialindex.so:devel/spatialindex \ libspatialite.so:databases/spatialite \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libxerces-c.so:textproc/xerces-c3 \ libzip.so:archivers/libzip \ libzstd.so:archivers/zstd RUN_DEPENDS= astyle:devel/astyle \ opencl>=0:devel/opencl \ ${PYTHON_PKGNAMEPREFIX}black>=19.10:devel/py-black@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}cycler>=0.10.0:devel/py-cycler@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dateutil>=2.8.1:devel/py-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Fiona>=0:graphics/py-fiona@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>=0.18.2:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}gdal>=3.1.0:graphics/py-gdal@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}geojson>=2.3.0:devel/py-geojson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}geopandas>=0.7.0:graphics/py-geopandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}httplib2>=0.17.3:www/py-httplib2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jedi>=0.12.1:devel/py-jedi@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=2.10.1:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}markupsafe>=1.1.1:textproc/py-markupsafe@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.4:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>=3.0.5:devel/py-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nbformat>=5.0.7:devel/py-nbformat@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=2.1:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nltk>=3.4.1:textproc/py-nltk@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0.24.1:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0.24.2:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pbr>=3.1.1:devel/py-pbr@${PY_FLAVOR} \ ${PY_PILLOW} \ ${PYTHON_PKGNAMEPREFIX}pip>=19.1.1:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plotly>=3.0.2:graphics/py-plotly@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}psutil>=5.7.0:sysutils/py-psutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}psycopg2>=2.8.5:databases/py-psycopg2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygments>=2.5.2:textproc/py-pygments@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyproj>=2.1.3:graphics/py-pyproj@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyrsgis>=0.2.6:graphics/py-pyrsgis@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytz>=2020.1:devel/py-pytz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}rasterio>=0:graphics/py-rasterio@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.22.0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-image>=0.14.3:graphics/py-scikit-image@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Shapely>=1.6.4:devel/py-shapely@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>=1.14.0:devel/py-six@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlite3>=3.7.7:databases/py-sqlite3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}termcolor>=1.1.0:devel/py-termcolor@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xlrd>=2.0.1:textproc/py-xlrd@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=5.3.1:devel/py-yaml@${PY_FLAVOR} ### Fortran is needed by numpy, GRASS, etc. USES= bison cmake compiler:features desktop-file-utils \ fortran gl gmake gnome pgsql pyqt:5 python:3.7+ qca qt:5 \ shebangfix sqlite:3 tar:bz2 USE_GL= gl USE_GNOME= libxml2 USE_LDCONFIG= yes USE_PYQT= pyqt5 qscintilla2 pysip sip USE_QT= 3d buildtools_build core concurrent dbus declarative \ designer_build qdoc_build gamepad gui linguist_build location \ network printsupport qmake_build script serialport \ sql sql-pgsql sql-sqlite3 svg uitools_build \ webengine webkit widgets xml SHEBANG_FILES= src/plugins/grass/scripts/*.py CMAKE_ARGS+= -DCMAKE_BUILD_TYPE:STRING=Release \ -DCMAKE_POLICY_DEFAULT_CMP0056:STRING=NEW \ -DLazPerf_INCLUDE_DIR:PATH=${LOCALBASE}/include/lazperf \ -DWITH_INTERNAL_MDAL:BOOL=false \ -DPYRCC_PROGRAM:FILEPATH=${LOCALBASE}/bin/pyrcc5-${PYTHON_VER} \ -DPYUIC_PROGRAM:FILEPATH=${LOCALBASE}/bin/pyuic5-${PYTHON_VER} \ -DQSCI_SIP_DIR:PATH=${PYQT_SIPDIR}/Qsci \ -DQWT_INCLUDE_DIR:PATH=${LOCALBASE}/include/qt5/qwt6 \ -DQWT_LIBRARY:FILEPATH=${LOCALBASE}/lib/qt5/libqwt6.so \ -DQGIS_MANUAL_SUBDIR:PATH=share/man CMAKE_ON= USE_OPENCL WITH_3D WITH_ASTYLE \ WITH_BINDINGS WITH_CUSTOM_WIDGETS WITH_EPT WITH_POSTGRESQL \ WITH_PDAL CMAKE_OFF= ENABLE_TESTS WITH_QWTPOLAR CONFLICTS_INSTALL= qgis PLIST_SUB= DISTVERSION=${DISTVERSION} .if !defined(MAINTAINER_MODE) CMAKE_ARGS+= -Wno-dev CMAKE_OFF+= SUPPRESS_QT_WARNINGS .endif OPTIONS_DEFINE= GRASS SERVER OPTIONS_DEFAULT= GRASS SERVER NO_OPTIONS_SORT= yes OPTIONS_SUB= yes SERVER_DESC= Enable QGIS server GRASS_BUILD_DEPENDS= grass7:databases/grass7 GRASS_RUN_DEPENDS= ${GRASS_BUILD_DEPENDS} GRASS_CMAKE_BOOL= WITH_GRASS7 SERVER_LIB_DEPENDS= libfcgi.so:www/fcgi SERVER_CMAKE_BOOL= WITH_SERVER WITH_SERVER_PLUGINS WITH_QSPATIALITE .include # QGIS requires flex >= 2.5.6, see # https://github.com/qgis/QGIS/blob/fb0f334b06e0828e5695ffcaa7c7eb82d6516cb0/INSTALL.md .if (${OPSYS} == FreeBSD && ${OSVERSION} < 1300501) BUILD_DEPENDS+= ${LOCALBASE}/bin/flex:textproc/flex CMAKE_ARGS+= -DFLEX_EXECUTABLE:FILEPATH=${LOCALBASE}/bin/flex .endif post-patch: # On i386, '-mllvm -inline-threshold=128' does not build under all circumstances # See bugs 242557 and 241687. .if ${OPSYS} == FreeBSD && ${ARCH} == "i386" @${REINPLACE_CMD} -e 's|"-mllvm -inline-threshold=128"|"-O1"|g' \ ${WRKSRC}/src/core/CMakeLists.txt .endif pre-configure: ${MKDIR} ${CONFIGURE_WRKSRC}/bin && ${LN} -s ${PYTHON_CMD} ${CONFIGURE_WRKSRC}/bin/python3 post-install: @${RM} ${STAGEDIR}${DATADIR}/python/pytz/tzfile.py.bak @${FIND} ${STAGEDIR}${LOCALBASE} -name "__pycache__" -delete @${RM} /tmp/srs.db check: @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} check .include diff --git a/graphics/qgis/Makefile b/graphics/qgis/Makefile index f7ba01ac3f65..a84b4d0407ad 100644 --- a/graphics/qgis/Makefile +++ b/graphics/qgis/Makefile @@ -1,182 +1,183 @@ # Created by: Laurent Courty PORTNAME= qgis DISTVERSION= 3.24.3 +PORTREVISION= 1 CATEGORIES= graphics geography MASTER_SITES= https://qgis.org/downloads/ MAINTAINER= rhurlin@FreeBSD.org COMMENT= Free and Open Source Geographic Information System LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/doc/LICENSE BUILD_DEPENDS= gpsbabel>=1.5.4:astro/gpsbabel \ opencl>=0:devel/opencl \ ${PYTHON_PKGNAMEPREFIX}cycler>=0.10.0:devel/py-cycler@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dateutil>=2.8.1:devel/py-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>=0.18.2:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}httplib2>=0.17.3:www/py-httplib2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=2.10.1:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}markupsafe>=1.1.1:textproc/py-markupsafe@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.4:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>=3.0.5:devel/py-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0.25.0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pbr>=3.1.1:devel/py-pbr@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pip>=19.1.1:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plotly>=3.0.2:graphics/py-plotly@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygments>=2.5.2:textproc/py-pygments@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyproj>=2.1.3:graphics/py-pyproj@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytz>=2020.1:devel/py-pytz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.22.0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>=1.14.0:devel/py-six@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlite3>=3.7.7:databases/py-sqlite3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=5.3.1:devel/py-yaml@${PY_FLAVOR} LIB_DEPENDS= libexiv2.so:graphics/exiv2 \ libexpat.so:textproc/expat2 \ libgdal.so:graphics/gdal \ libgeos.so:graphics/geos \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ liblazperf.so:archivers/lazperf \ libmdal.so:math/mdal \ libnetcdf.so:science/netcdf \ libOpenCL.so:devel/ocl-icd \ libpdal_base.so:math/pdal \ libproj.so:graphics/proj \ libprotobuf-lite.so:devel/protobuf \ libqjson-qt5.so:devel/qjson \ libqscintilla2_qt5.so:devel/qscintilla2-qt5 \ libqt5keychain.so:security/qtkeychain \ libqwt6.so:x11-toolkits/qwt6 \ libspatialindex.so:devel/spatialindex \ libspatialite.so:databases/spatialite \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libxerces-c.so:textproc/xerces-c3 \ libzip.so:archivers/libzip \ libzstd.so:archivers/zstd RUN_DEPENDS= astyle:devel/astyle \ opencl>=0:devel/opencl \ ${PYTHON_PKGNAMEPREFIX}black>=19.10:devel/py-black@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}cycler>=0.10.0:devel/py-cycler@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dateutil>=2.8.1:devel/py-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Fiona>=0:graphics/py-fiona@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}future>=0.18.2:devel/py-future@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}gdal>=3.1.0:graphics/py-gdal@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}geojson>=2.3.0:devel/py-geojson@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}geopandas>=0.7.0:graphics/py-geopandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}httplib2>=0.17.3:www/py-httplib2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}jedi>=0.12.1:devel/py-jedi@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Jinja2>=2.10.1:devel/py-Jinja2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}markupsafe>=1.1.1:textproc/py-markupsafe@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.2.4:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}mock>=3.0.5:devel/py-mock@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nbformat>=5.0.7:devel/py-nbformat@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>=2.1:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nltk>=3.4.1:textproc/py-nltk@${PY_FLAVOR} \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}OWSLib>=0.25.0:graphics/py-OWSLib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=0.24.2:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pbr>=3.1.1:devel/py-pbr@${PY_FLAVOR} \ ${PY_PILLOW} \ ${PYTHON_PKGNAMEPREFIX}pip>=19.1.1:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}plotly>=3.0.2:graphics/py-plotly@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}psutil>=5.7.0:sysutils/py-psutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}psycopg2>=2.8.5:databases/py-psycopg2@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pygments>=2.5.2:textproc/py-pygments@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyproj>=2.1.3:graphics/py-pyproj@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyrsgis>=0.2.6:graphics/py-pyrsgis@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pytz>=2020.1:devel/py-pytz@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}rasterio>=0:graphics/py-rasterio@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>=2.22.0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-image>=0.14.3:graphics/py-scikit-image@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}Shapely>=1.6.4:devel/py-shapely@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}six>=1.14.0:devel/py-six@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}sqlite3>=3.7.7:databases/py-sqlite3@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}termcolor>=1.1.0:devel/py-termcolor@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xlrd>=2.0.1:textproc/py-xlrd@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>=5.3.1:devel/py-yaml@${PY_FLAVOR} ### Fortran is needed by numpy, GRASS, etc. USES= bison cmake compiler:features desktop-file-utils \ fortran gl gmake gnome pgsql pyqt:5 python:3.7+ qca qt:5 \ shebangfix sqlite:3 tar:bz2 USE_GL= gl USE_GNOME= libxml2 USE_LDCONFIG= yes USE_PYQT= pyqt5 qscintilla2 pysip sip USE_QT= 3d buildtools_build core concurrent dbus declarative \ designer_build qdoc_build gamepad gui linguist_build location \ network printsupport qmake_build script serialport \ sql sql-pgsql sql-sqlite3 svg uitools_build \ webengine webkit widgets xml SHEBANG_FILES= src/plugins/grass/scripts/*.py CMAKE_ARGS+= -DCMAKE_BUILD_TYPE:STRING=Release \ -DCMAKE_POLICY_DEFAULT_CMP0056:STRING=NEW \ -DLazPerf_INCLUDE_DIR:PATH=${LOCALBASE}/include/lazperf \ -DWITH_INTERNAL_MDAL:BOOL=false \ -DPYRCC_PROGRAM:FILEPATH=${LOCALBASE}/bin/pyrcc5-${PYTHON_VER} \ -DPYUIC_PROGRAM:FILEPATH=${LOCALBASE}/bin/pyuic5-${PYTHON_VER} \ -DQSCI_SIP_DIR:PATH=${PYQT_SIPDIR}/Qsci \ -DQWT_INCLUDE_DIR:PATH=${LOCALBASE}/include/qt5/qwt6 \ -DQWT_LIBRARY:FILEPATH=${LOCALBASE}/lib/qt5/libqwt6.so \ -DQGIS_MANUAL_SUBDIR:PATH=share/man CMAKE_ON= USE_OPENCL WITH_3D WITH_ASTYLE \ WITH_BINDINGS WITH_CUSTOM_WIDGETS WITH_EPT WITH_POSTGRESQL \ WITH_PDAL CMAKE_OFF= ENABLE_TESTS WITH_QWTPOLAR CONFLICTS_INSTALL= qgis-ltr PLIST_SUB= DISTVERSION=${PORTVERSION} .if !defined(MAINTAINER_MODE) CMAKE_ARGS+= -Wno-dev CMAKE_OFF+= SUPPRESS_QT_WARNINGS .endif OPTIONS_DEFINE= GRASS SERVER OPTIONS_DEFAULT= GRASS SERVER NO_OPTIONS_SORT= yes OPTIONS_SUB= yes SERVER_DESC= Enable QGIS server GRASS_BUILD_DEPENDS= grass7:databases/grass7 GRASS_RUN_DEPENDS= ${GRASS_BUILD_DEPENDS} GRASS_CMAKE_BOOL= WITH_GRASS7 SERVER_LIB_DEPENDS= libfcgi.so:www/fcgi SERVER_CMAKE_BOOL= WITH_SERVER WITH_SERVER_PLUGINS WITH_QSPATIALITE .include # QGIS requires flex >= 2.5.6, see # https://github.com/qgis/QGIS/blob/fb0f334b06e0828e5695ffcaa7c7eb82d6516cb0/INSTALL.md .if (${OPSYS} == FreeBSD && ${OSVERSION} < 1300501) BUILD_DEPENDS+= ${LOCALBASE}/bin/flex:textproc/flex CMAKE_ARGS+= -DFLEX_EXECUTABLE:FILEPATH=${LOCALBASE}/bin/flex .endif post-patch: # On i386, '-mllvm -inline-threshold=128' does not build under all circumstances # See bugs 242557 and 241687. .if ${OPSYS} == FreeBSD && ${ARCH} == "i386" @${REINPLACE_CMD} -e 's|"-mllvm -inline-threshold=128"|"-O1"|g' \ ${WRKSRC}/src/core/CMakeLists.txt .endif pre-configure: ${MKDIR} ${CONFIGURE_WRKSRC}/bin && ${LN} -s ${PYTHON_CMD} ${CONFIGURE_WRKSRC}/bin/python3 post-install: @${RM} ${STAGEDIR}${DATADIR}/python/pytz/tzfile.py.bak @${FIND} ${STAGEDIR}${LOCALBASE} -name "__pycache__" -delete @${RM} /tmp/srs.db check: @cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} check .include diff --git a/graphics/vigra/Makefile b/graphics/vigra/Makefile index 8199e7f767ed..b0c6be34fec8 100644 --- a/graphics/vigra/Makefile +++ b/graphics/vigra/Makefile @@ -1,77 +1,77 @@ # Created by: cartola (Carlos E. G. Carvalho) PORTNAME= vigra DISTVERSIONPREFIX=v DISTVERSION= 1.11.1 -PORTREVISION= 20 +PORTREVISION= 21 CATEGORIES= graphics MAINTAINER= ports@FreeBSD.org COMMENT= VIGRA stands for "Vision with Generic Algorithms" LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libImath.so:math/Imath \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake compiler:c++14-lang python:run shebangfix USE_GITHUB= yes GH_ACCOUNT= ukoethe GH_TAGNAME= 8acd73a USE_LDCONFIG= yes CFLAGS+= -I${LOCALBASE}/include/Imath CMAKE_ARGS= -DDEPENDENCY_SEARCH_PREFIX:PATH=${LOCALBASE} \ -DDOCINSTALL:PATH=${DOCSDIR_REL} SHEBANG_FILES= config/vigra-config.in OPTIONS_DEFINE= HDF5 OPENEXR NUMPY DOCS FFTW OPTIONS_DEFAULT= HDF5 OPENEXR FFTW ${OPTIONS_GROUP_IMAGEFORMATS} OPTIONS_GROUP= IMAGEFORMATS OPTIONS_GROUP_IMAGEFORMATS= PNG JPEG TIFF OPTIONS_SUB= yes HDF5_CMAKE_BOOL= WITH_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 OPENEXR_CMAKE_BOOL= WITH_OPENEXR OPENEXR_LIB_DEPENDS= libOpenEXR.so:graphics/openexr NUMPY_DESC= NumPy mathematical computing (USE Fortran/GCC47+) NUMPY_CMAKE_BOOL= WITH_VIGRANUMPY NUMPY_USES= compiler:gcc-c++11-lib python:build NUMPY_BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} \ ${PYNUMPY} NUMPY_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} \ ${PYNUMPY} NUMPY_LIB_DEPENDS= ${PY_BOOST} # On FreeBSD < 11 libc++ lacks support for sized delete operators. # GCC dropped the builtin version of these operators in 6+ by # defaulting to gnu++14. Force c++11 instead. # For a more detailed discussion see: # https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=219484 NUMPY_CXXFLAGS= -std=gnu++11 PNG_CMAKE_BOOL= WITH_PNG PNG_LIB_DEPENDS= libpng.so:graphics/png JPEG_CMAKE_BOOL= WITH_JPEG JPEG_USES= jpeg TIFF_CMAKE_BOOL= WITH_TIFF TIFF_LIB_DEPENDS= libtiff.so:graphics/tiff FFTW_CMAKE_BOOL= WITH_FFTW FFTW_LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float post-package-NUMPY-on: @${ECHO} "" @${ECHO} "* BEWARE!" @${ECHO} "* Using py-NumPY implies Fortran and GCC 4.7+ as hard dependencies" @${ECHO} "* and require all ports, depending on vigra, to set USE_GCC=yes" @${ECHO} "" .include diff --git a/graphics/vv/Makefile b/graphics/vv/Makefile index ff8f75db3ed0..498d345b932c 100644 --- a/graphics/vv/Makefile +++ b/graphics/vv/Makefile @@ -1,45 +1,45 @@ PORTNAME= vv DISTVERSIONPREFIX= v DISTVERSION= 1.4.0-383 DISTVERSIONSUFFIX= -g7a783a8b -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= graphics MAINTAINER= yuri@FreeBSD.org COMMENT= Fast and simple 4D image viewer LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= googletest>0:devel/googletest # error: unable to find library -lGTest::GTest, see https://github.com/open-vv/vv/issues/74 LIB_DEPENDS= libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libgdcmCommon.so:devel/gdcm \ libhdf5_cpp.so:science/hdf5 \ libITKLabelMap-5.0.so:science/InsightToolkit \ libpng.so:graphics/png \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libtiff.so:graphics/tiff \ libvtkIOSQL-8.2.so:math/vtk8 USES= cmake compiler:c++11-lang eigen:3 jpeg qt:5 xorg USE_GITHUB= yes GH_ACCOUNT= open-vv USE_QT= core designer gui network sql widgets xml buildtools_build qmake_build USE_XORG= ice sm x11 xext xt USE_CXXSTD= c++11 CMAKE_ARGS= -DVTK_DIR:PATH=${LOCALBASE}/lib/vtk-8.2/cmake/vtk-8.2 PLIST_FILES= bin/vv .include .if ${ARCH} == i386 CXXFLAGS+= -msse2 # workaround for ITK failing to add -msse2 on i386: https://github.com/open-vv/vv/issues/83 & https://github.com/InsightSoftwareConsortium/ITK/issues/2011 .endif post-configure: # workaround for "error: unable to find library -lGTest::GTest", see https://github.com/open-vv/vv/issues/74 @${REINPLACE_CMD} -E 's/ -lGTest::(GTest|Main) / /g' ${BUILD_WRKSRC}/build.ninja .include diff --git a/math/ambit/Makefile b/math/ambit/Makefile index 8a5940ccc07a..f596c0e5f59d 100644 --- a/math/ambit/Makefile +++ b/math/ambit/Makefile @@ -1,28 +1,29 @@ PORTNAME= ambit DISTVERSIONPREFIX= v DISTVERSION= 0.6 +PORTREVISION= 1 CATEGORIES= math PKGNAMESUFFIX= -tensor # avoid clash with shells/ambit MAINTAINER= yuri@FreeBSD.org COMMENT= C++ library for tensor product calculations LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libhdf5.so:science/hdf5 \ libopenblas.so:math/openblas \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake:testing compiler:c++11-lang python:build USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= jturney # some declared cmake options do nothing: see https://github.com/jturney/ambit/issues/25 and the patch CMAKE_ON= SHARED_ONLY ENABLE_OPENMP CMAKE_OFF= ENABLE_TESTS # https://github.com/jturney/ambit/issues/24 CMAKE_TESTING_ON= ENABLE_TESTS .include diff --git a/math/armadillo/Makefile b/math/armadillo/Makefile index d44c4169d02b..3678da6576f0 100644 --- a/math/armadillo/Makefile +++ b/math/armadillo/Makefile @@ -1,24 +1,25 @@ PORTNAME= armadillo PORTVERSION= 11.2.0 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= SF/arma MAINTAINER= salvadore@FreeBSD.org COMMENT= C++ linear algebra library LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libarpack.so:math/arpack-ng \ libboost_date_time.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ liblapack.so:math/lapack \ libsuperlu.so:math/superlu \ - libsz.so:science/szip + libsz.so:science/libaec USES= blaslapack:openblas cmake compiler:c++11-lang pkgconfig tar:xz USE_LDCONFIG= yes CMAKE_ARGS+= -DPKG_CONFIG_DIR=${LOCALBASE}/libdata/pkgconfig/ .include diff --git a/math/flann/Makefile b/math/flann/Makefile index 8de1262028ac..30114a68bcb3 100644 --- a/math/flann/Makefile +++ b/math/flann/Makefile @@ -1,27 +1,28 @@ PORTNAME= flann DISTVERSION= 1.9.2 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Library for fast nearest neighbor searches in high dimensional spaces LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libhdf5.so:science/hdf5 \ liblz4.so:archivers/liblz4 \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake compiler:c++11-lang localbase:ldflags pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= tkircher CMAKE_OFF= BUILD_PYTHON_BINDINGS BUILD_MATLAB_BINDINGS BUILD_EXAMPLES BUILD_TESTS BUILD_DOC \ USE_OPENMP # OpenMP search is broken in cmake: https://gitlab.kitware.com/cmake/cmake/issues/17474 post-install: # workaround for https://github.com/mariusmuja/flann/issues/466 ${REINPLACE_CMD} -i '' -e 's/lib;-llz4/lib -llz4/' ${STAGEDIR}${PREFIX}/libdata/pkgconfig/flann.pc .include diff --git a/math/freefem++/Makefile b/math/freefem++/Makefile index 1327f4483769..87c8007a9ac2 100644 --- a/math/freefem++/Makefile +++ b/math/freefem++/Makefile @@ -1,75 +1,76 @@ # Created by: Thierry Thomas PORTNAME= freefem++ DISTVERSIONPREFIX= v DISTVERSION= 4.11 +PORTREVISION= 1 CATEGORIES= math science MAINTAINER= yuri@FreeBSD.org COMMENT= Partial differential equation solver 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 \ - libsz.so:science/szip + libsz.so:science/libaec RUN_DEPENDS= bash:shells/bash \ pipe:misc/pipe USES= autoreconf bison blaslapack:openblas compiler:c++11-lib 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${LOCALBASE}/include/superlu .if !defined{WITH_DEBUG} LDFLAGS+= -s .endif GNU_CONFIGURE= yes CONFIGURE_ENV= CNOFLAGS="${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 pre-configure: @${REINPLACE_CMD} -e 's|-llapack|${LAPACKLIB}|' ${WRKSRC}/configure.ac post-install: @${MV} ${STAGEDIR}${DATADIR}/examples ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/math/labplot/Makefile b/math/labplot/Makefile index a37a37fdaf09..67eea7aa4932 100644 --- a/math/labplot/Makefile +++ b/math/labplot/Makefile @@ -1,62 +1,62 @@ # Created by: Kay Lehmann PORTNAME= labplot DISTVERSION= 2.8.2 -PORTREVISION= 16 +PORTREVISION= 17 CATEGORIES= math kde MASTER_SITES= KDE/stable/${PORTNAME}/${PORTVERSION} PATCH_SITES= https://invent.kde.org/education/labplot/-/commit/ PATCHFILES= 375786ca124a1a6773c609236f8341890f23e1d8.diff:-p1 \ 9e77b593030fdae0fbbad113415483b3ca51a654.diff:-p1 MAINTAINER= kde@FreeBSD.org COMMENT= Data plotting and function analysis tool by KDE LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libgsl.so:math/gsl \ liblz4.so:archivers/liblz4 \ libspectre.so:print/libspectre \ - libsz.so:science/szip + libsz.so:science/libaec USES= bison cmake compiler:c++11-lang desktop-file-utils kde:5 qt:5 \ shared-mime-info tar:xz USE_KDE= archive attica auth bookmarks codecs completion config configwidgets \ coreaddons crash guiaddons i18n iconthemes itemviews \ jobwidgets kio newstuff notifications parts \ service solid sonnet syntaxhighlighting textwidgets unitconversion \ widgetsaddons windowsystem xmlgui \ doctools_build ecm_build USE_QT= concurrent core dbus gui network printsupport serialport \ sql svg widgets xml \ buildtools_build qmake_build testlib_build CMAKE_OFF= ENABLE_LIBCERF CMAKE_ON= CMAKE_DISABLE_FIND_PACKAGE_KUserFeedback DATADIR= ${PREFIX}/share/labplot2 OPTIONS_DEFINE= CANTOR FITS FFTW3 HDF5 NETCDF OPTIONS_DEFAULT= ${OPTIONS_DEFINE} CANTOR_DESC= Build with Cantor support CANTOR_CMAKE_BOOL= ENABLE_CANTOR CANTOR_LIB_DEPENDS= libcantorlibs.so:math/cantor \ libpoppler.so:graphics/poppler \ libpoppler-qt5.so:graphics/poppler-qt5 FITS_DESC= Flexible Image Transport System Data Format (FITS) Library FITS_CMAKE_BOOL= ENABLE_FITS FITS_LIB_DEPENDS= libcfitsio.so:astro/cfitsio FFTW3_DESC= Build with FFTW support FFTW3_CMAKE_BOOL= ENABLE_FFTW FFTW3_LIB_DEPENDS= libfftw3.so:math/fftw3 HDF5_DESC= Build with HDF5 support HDF5_CMAKE_BOOL= ENABLE_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 NETCDF_DESC= Build with NetCDF support NETCDF_CMAKE_BOOL= ENABLE_NETCDF NETCDF_LIB_DEPENDS= libnetcdf.so:science/netcdf .include diff --git a/math/mathgl/Makefile b/math/mathgl/Makefile index 79d0992bae49..c58a726f7c2c 100644 --- a/math/mathgl/Makefile +++ b/math/mathgl/Makefile @@ -1,85 +1,85 @@ PORTNAME= mathgl DISTVERSION= 2.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math graphics MASTER_SITES= SF/${PORTNAME}/${PORTNAME}/${PORTNAME}%20${PORTVERSION}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Library for high-quality scientific data visualization LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libgif.so:graphics/giflib \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ libhpdf.so:print/libharu \ libltdl.so:devel/libltdl \ libpng.so:graphics/png \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake compiler:c++11-lang gettext-runtime gl jpeg xorg USE_GL= gl glu glut USE_XORG= xi xmu USE_LDCONFIG= yes .for v in double gif glut gsl hdf5 jpeg ltdl mgl2 opengl pdf png zlib CMAKE_ARGS+= -Denable-${v}=ON .endfor .for v in doc-info doc-html lgpl mgltex CMAKE_ARGS+= -Denable-${v}=OFF .endfor OPTIONS_DEFINE= PYTHON MPI OPTIONS_GROUP= GRAPHICS OPTIONS_GROUP_GRAPHICS= QT5 FLTK WXGTK OPTIONS_RADIO= THREADS OPTIONS_RADIO_THREADS= PTHREADS OPENMP OPTIONS_DEFAULT= QT5 OPTIONS_SUB= yes GRAPHICS_DESC= Graphics support PTHREADS_DESC= Enable POSIX threads support (broken, fix pending release) OPENMP_DESC= Parallel processing support via OpenMP (broken, cmake bug) FLTK_DESC= Enable fltk widget PLIST_SUB= SHLIB_VER=7.6.0 PYTHON_CMAKE_BOOL= enable-python PYTHON_BUILD_DEPENDS= swig:devel/swig \ ${PYNUMPY} PYTHON_RUN_DEPENDS= ${PYNUMPY} PYTHON_BROKEN= Python option needs to be fixed: lgpl needs to be enabled for it MPI_CMAKE_BOOL= enable-mpi MPI_LIB_DEPENDS= libmpi.so:net/openmpi QT5_CMAKE_BOOL= enable-qt5 QT5_USE= QT=core,gui,opengl,printsupport,widgets,buildtools_build,qmake_build QT5_USES= desktop-file-utils qt:5 shared-mime-info FLTK_CMAKE_BOOL= enable-fltk FLTK_LIB_DEPENDS= libfltk.so:x11-toolkits/fltk FLTK_USE= XORG=ice,sm,x11,xext WXGTK_CMAKE_BOOL= wx WXGTK_USE= WX=3.0+ OPENMP_CMAKE_BOOL= enable-openmp PTHREADS_CMAKE_BOOL= enable-pthread .include .if ! ${PORT_OPTIONS:MFLTK} && ! ${PORT_OPTIONS:MQT5} PLIST_SUB+= FLTK_OR_QT5="@comment " .else PLIST_SUB+= FLTK_OR_QT5="" .endif .if ${PORT_OPTIONS:MFLTK} && ${PORT_OPTIONS:MQT5} PLIST_SUB+= FLTK_AND_QT5="" .else PLIST_SUB+= FLTK_AND_QT5="@comment " .endif .include diff --git a/math/mdal/Makefile b/math/mdal/Makefile index 9b46205fb112..c6580aa2614a 100644 --- a/math/mdal/Makefile +++ b/math/mdal/Makefile @@ -1,39 +1,40 @@ # Created by: Wen Heping PORTNAME= mdal DISTVERSION= 0.9.4 +PORTREVISION= 1 CATEGORIES= math geography MAINTAINER= wen@FreeBSD.org COMMENT= Mesh data abstration library LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${LOCALBASE}/include/gtest/gtest.h:devel/googletest LIB_DEPENDS= libpdal_base.so:math/pdal \ libnetcdf.so:science/netcdf \ libsqlite3.so:databases/sqlite3 \ libgdal.so:graphics/gdal \ libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake gnome localbase USE_GNOME= libxml2 USE_LDCONFIG= yes PLIST_FILES= bin/mdal_translate \ bin/mdalinfo \ include/mdal.h \ lib/libmdal.so \ lib/libmdal_a.a USE_GITHUB= yes GH_ACCOUNT= lutraconsulting GH_PROJECT= MDAL GH_TAGNAME= release-${DISTVERSION} CMAKE_ARGS= -DSQLITE3_INCLUDE_DIRS="${LOCALBASE}/include" \ -DSQLITE3_LIBRARY="${LOCALBASE}/lib/libsqlite3.so" .include diff --git a/math/openturns/Makefile b/math/openturns/Makefile index e4615c26d033..b2c071adb738 100644 --- a/math/openturns/Makefile +++ b/math/openturns/Makefile @@ -1,100 +1,100 @@ PORTNAME= openturns DISTVERSIONPREFIX= v DISTVERSION= 1.19 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Uncertainty treatment library LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/COPYING.LESSER BUILD_DEPENDS= boost-libs>0:devel/boost-libs \ flex:textproc/flex \ spectra>0:math/spectra LIB_DEPENDS= libamd.so:math/suitesparse-amd \ libblas.so:math/blas \ libbonmin.so:math/bonmin \ libboost_serialization.so:devel/boost-libs \ libcamd.so:math/suitesparse-camd \ libceres.so:math/ceres-solver \ libCbc.so:math/cbc \ libccolamd.so:math/suitesparse-ccolamd \ libCgl.so:math/cgl \ libcholmod.so:math/suitesparse-cholmod \ libClp.so:math/clp \ libcminpack.so:math/cminpack \ libcoinasl.so:math/asl \ libCoinUtils.so:math/coinutils \ libcolamd.so:math/suitesparse-colamd \ libcxsparse.so:math/suitesparse-cxsparse \ libdlib.so:science/dlib-cpp \ libgif.so:graphics/giflib \ libgflags.so:devel/gflags \ libglog.so:devel/glog \ libgmp.so:math/gmp \ libhdf5_cpp.so:science/hdf5 \ libipopt.so:math/ipopt \ liblapack.so:math/lapack \ libmetis.so:math/metis \ libmpc.so:math/mpc \ libmpfr.so:math/mpfr \ libnauty.so:math/nauty \ libnlopt.so:math/nlopt \ libOsi.so:math/osi \ libpagmo.so:science/pagmo2 \ libpng16.so:graphics/png \ libprimesieve.so:math/primesieve \ libspqr.so:math/suitesparse-spqr \ libsuitesparseconfig.so:math/suitesparse-config \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libtbb.so:devel/onetbb \ libunwind.so:devel/libunwind USES= bison blaslapack:openblas cmake eigen:3 gnome jpeg localbase:ldflags pkgconfig sqlite xorg # compiler:c++17-lang USE_GITHUB= yes USE_GNOME= libxml2 USE_XORG= ice sm x11 xau xcb xdmcp xext USE_LDCONFIG= yes CMAKE_ARGS= -DBLAS_LIBRARIES=${LOCALBASE}/lib/libopenblas.so -DLAPACK_LIBRARIES=${LOCALBASE}/lib/libopenblas.so \ -DOPENTURNS_EXAMPLE_PATH:STRING=share/examples/openturns \ -DOPENTURNS_DOC_PATH:STRING=share/doc/openturns CMAKE_OFF= USE_DOXYGEN USE_SPHINX CMAKE_OFF+= USE_HMAT # broken with hmat-oss-1.7.1: https://github.com/openturns/openturns/issues/1868 TEST_TARGET= check # 10 tests are known to fail: https://github.com/openturns/openturns/issues/1919 OPTIONS_DEFINE= PYTHON EXAMPLES OPTIONS_DEFAULT= PYTHON OPTIONS_SUB= yes PYTHON_USES= python PYTHON_CMAKE_BOOL= BUILD_PYTHON PYTHON_CMAKE_ON= -DSWIG_EXECUTABLE=${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} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${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/pdal/Makefile b/math/pdal/Makefile index d9760708c942..d37f817a5ac4 100644 --- a/math/pdal/Makefile +++ b/math/pdal/Makefile @@ -1,79 +1,79 @@ # Created by: bart PORTNAME= pdal DISTVERSION= 2.3.0 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= math databases graphics MASTER_SITES= https://github.com/PDAL/PDAL/releases/download/${DISTVERSION}/ DISTNAME= ${PORTNAME}-${DISTVERSION}-src MAINTAINER= lbartoletti@FreeBSD.org COMMENT= Library for translating and manipulating point cloud data LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= nlohmann-json>0:devel/nlohmann-json LIB_DEPENDS= libgdal.so:graphics/gdal \ libgeos.so:graphics/geos \ libboost_thread.so:devel/boost-libs \ libcurl.so:ftp/curl \ libgeotiff.so:graphics/libgeotiff \ libxml2.so:textproc/libxml2 \ liblaszip.so:archivers/laszip \ libzstd.so:archivers/zstd \ ${LIB_DEPENDS_${ARCH}} LIB_DEPENDS_aarch64= libunwind.so:devel/libunwind LIB_DEPENDS_amd64= libunwind.so:devel/libunwind LIB_DEPENDS_armv7= libunwind.so:devel/libunwind LIB_DEPENDS_i386= libunwind.so:devel/libunwind LIB_DEPENDS_powerpc64= libunwind.so:devel/libunwind LIB_DEPENDS_powerpc64le=libunwind.so:devel/libunwind USES= cmake compiler:c++11-lib pathfix pkgconfig ssl tar:bz2 USE_LDCONFIG= yes WRKSRC= ${WRKDIR}/${PORTNAME:tu}-${DISTVERSION}-src CMAKE_ON= WITH_LASZIP #LASZIP is recommended CMAKE_OFF= WITH_TESTS OPTIONS_DEFINE= BASH \ ICEBRIDGE PGPOINTCLOUD LAZPERF MBIO \ OPTIONS_DEFAULT= BASH \ ICEBRIDGE PGPOINTCLOUD LAZPERF MBIO #Plugins with lib not in port: #RivLib, Matlab, MrSID, CPD, GeoWave, GreyHound, HexBin, NITF (nitro) OPTIONS_SUB= yes BASH_DESC= BASH completion ICEBRIDGE_DESC= Enable Icebridge plugin LAZPERF_DESC= Enable LAZPerf plugin MBIO_DESC= Enable MBIO plugin PGPOINTCLOUD_DESC= Enable Coherent PostgreSQL Point Cloud plugin BASH_CMAKE_BOOL= WITH_COMPLETION BASH_RUN_DEPENDS= bash:shells/bash ICEBRIDGE_CMAKE_BOOL= BUILD_PLUGIN_ICEBRIDGE ICEBRIDGE_LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec LAZPERF_CMAKE_BOOL= WITH_LAZPERF LAZPERF_LIB_DEPENDS= liblazperf.so:archivers/lazperf MBIO_CMAKE_BOOL= BUILD_PLUGIN_MBIO PGPOINTCLOUD_CMAKE_BOOL= BUILD_PLUGIN_PGPOINTCLOUD PGPOINTCLOUD_USES= pgsql CXXFLAGS_powerpc64= -mvsx post-install-BASH-on: ${MKDIR} ${STAGEDIR}${PREFIX}/share/bash-completion/completions ${INSTALL_DATA} ${WRKSRC}/scripts/bash-completion/pdal \ ${STAGEDIR}${PREFIX}/share/bash-completion/completions .include diff --git a/math/saga/Makefile b/math/saga/Makefile index 0b1ddf09b913..c124604fbc06 100644 --- a/math/saga/Makefile +++ b/math/saga/Makefile @@ -1,97 +1,98 @@ # Created by: Rainer Hurling PORTNAME= saga PORTVERSION= 8.2.2 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= SF/saga-gis/SAGA%20-%20${PORTVERSION:C/\.[[:digit:]]\.[[:digit:]]*$//}/SAGA%20-%20${PORTVERSION} MAINTAINER= rhurlin@FreeBSD.org COMMENT= System for Automated Geoscientific Analyses LICENSE= GPLv2 LGPL21 LICENSE_COMB= multi BUILD_DEPENDS= clang${LLVM_DEFAULT}:devel/llvm${LLVM_DEFAULT} \ swig:devel/swig LIB_DEPENDS= libcurl.so:ftp/curl \ libfftw3.so:math/fftw3 \ libgdal.so:graphics/gdal \ libhdf5.so:science/hdf5 \ libhpdf.so:print/libharu \ libjasper.so:graphics/jasper \ libodbc.so:databases/unixODBC \ libopencv_core.so:graphics/opencv \ libpdal_base.so:math/pdal \ libproj.so:graphics/proj \ libqhull_r.so:math/qhull \ libsvm.so:science/libsvm \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libtiff.so:graphics/tiff RUN_DEPENDS:= swig:devel/swig USES= cmake compiler:c++11-lib dos2unix gnome \ iconv:wchar_t libtool localbase pkgconfig python DOS2UNIX_GLOB= *.cpp *.h USE_LDCONFIG= yes USE_WX= 3.1+ CMAKE_ARGS+= -DSVM_INCLUDE:PATH=${LOCALBASE}/include/svm.h CMAKE_ON= WITH_DEV_TOOLS WITH_EXCERCISES WITH_MRMR WITH_SYSTEM_SVM CMAKE_ON+= CMAKE_VERBOSE_MAKEFILE CMAKE_OFF+= WITH_TOOLS_LAS WITH_TRIANGLE WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/saga-gis PLIST_SUB= PORTVERSION=${PORTVERSION} OPTIONS_DEFINE= PGSQL OPENMP VIGRA OPTIONS_DEFAULT= PGSQL VIGRA OPTIONS_DEFAULT_amd64= OPENMP OPTIONS_DEFAULT_i386= OPENMP OPTIONS_DEFAULT_powerpc64= OPENMP OPTIONS_DEFAULT_powerpc64le= OPENMP NO_OPTIONS_SORT= yes OPTIONS_SUB= yes OPENMP_DESC= Enable Multiprocessing (only amd64, i386 and powerpc64*) VIGRA_DESC= Enable 'Vision with Generic Algorithms' Library OPENMP_CONFIGURE_ENABLE= openmp PGSQL_USES= pgsql PGSQL_CONFIGURE_WITH= postgresql VIGRA_BUILD_DEPENDS= ${LOCALBASE}/lib/libvigraimpex.so:graphics/vigra VIGRA_RUN_DEPENDS= ${LOCALBASE}/lib/libvigraimpex.so:graphics/vigra .include # make describe needs them here CPP= clang-cpp${LLVM_DEFAULT} CC= clang${LLVM_DEFAULT} CXX= clang++${LLVM_DEFAULT} SUB_FILES= pkg-message post-patch: .if ${ARCH} == "powerpc" @${REINPLACE_CMD} -e 's|typedef unsigned long DWORD;|typedef unsigned int DWORD;|' \ ${WRKSRC}/src/saga_core/saga_api/api_core.h .endif @${REINPLACE_CMD} -e 's|PORTVERSION|${PORTVERSION}|' \ ${WRKSRC}/src/saga_core/saga_gui/dlg_about.cpp @${REINPLACE_CMD} -e 's|-lgomp|-lomp|' \ ${WRKSRC}/src/accessories/templates/template4saga-tools/my_tool_library/Makefile post-install: ${MKDIR} ${STAGEDIR}${DATADIR} ${INSTALL_DATA} ${WRKSRC}/src/saga_core/saga_gui/res/saga*.txt ${STAGEDIR}${DATADIR} ${INSTALL_DATA} ${WRKSRC}/src/saga_core/saga_gui/res/saga.png ${STAGEDIR}${DATADIR} ${RM} ${STAGEDIR}${DATADIR}/saga_dic.txt ${STAGEDIR}${DATADIR}/saga_srs.txt # toolchains dir was moved in r2805 (and followups r2810,r2811,r2820) (cd ${WRKSRC}/src/accessories && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}) ${RM} -R ${STAGEDIR}${DATADIR}/CMakeLists.txt ${RM} -R ${STAGEDIR}${DATADIR}/templates/template4saga-tools/my_tool_library/Makefile.bak ${INSTALL_DATA} ${WRKSRC}/src/saga_core/saga_gui/res/saga.desktop \ ${STAGEDIR}${PREFIX}/share/applications/ # library helper files are not needed and cripple some math/qgis extensions @${RM} ${STAGEDIR}${PREFIX}/lib/saga/*.la .include diff --git a/misc/adios2/Makefile b/misc/adios2/Makefile index 9887fabbd772..f4826ef0583a 100644 --- a/misc/adios2/Makefile +++ b/misc/adios2/Makefile @@ -1,56 +1,57 @@ PORTNAME= adios2 DISTVERSIONPREFIX= v DISTVERSION= 2.8.1 +PORTREVISION= 1 CATEGORIES= misc science MAINTAINER= yuri@FreeBSD.org COMMENT= Next generation of ADIOS developed in the Exascale Computing Program LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= constant expression evaluates to 18446744073709551613 which cannot be narrowed to type 'unsigned int': https://github.com/ornladios/ADIOS2/issues/2469 BROKEN_powerpc= constant expression evaluates to 18446744073709551613 which cannot be narrowed to type 'unsigned int': https://github.com/ornladios/ADIOS2/issues/2469 PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}mpi4py>=3.0.3:net/py-mpi4py@${PY_FLAVOR} BUILD_DEPENDS= bash:shells/bash \ pybind11>0:devel/pybind11 \ ${PYTHON_PKGNAMEPREFIX}pybind11>=2.4:devel/py-pybind11@${PY_FLAVOR} \ ${PY_DEPENDS} LIB_DEPENDS= libblosc.so:archivers/c-blosc \ libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libffi.so:devel/libffi \ libhdf5.so:science/hdf5 \ libmpi.so:net/mpich \ libpng.so:graphics/png \ libsodium.so:security/libsodium \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libzmq.so:net/libzmq4 \ libzfp.so:devel/zfp RUN_DEPENDS= bash:shells/bash \ ${PY_DEPENDS} USES= bison cmake:testing compiler:c++11-lang fortran localbase:ldflags pkgconfig \ perl5 python shebangfix USE_LDCONFIG= yes SHEBANG_FILES= cmake/install/post/adios2-config.pre.sh.in cmake/install/post/generate-adios2-config.sh.in \ source/utils/adios_reorganize/adios2_reorganize_wrapper source/utils/adios2_deactivate_bp SHEBANG_GLOB= *.sh *.py USE_GITHUB= yes GH_ACCOUNT= ornladios GH_PROJECT= ADIOS2 CMAKE_ARGS= -DFREEBSD_PYTHON_VERSION=${PYTHON_VER} CMAKE_OFF= BUILD_TESTING LDFLAGS+= -lepoll-shim OPTIONS_DEFINE= DOCS DOCSDIR= ${PREFIX}/share/doc/ADIOS2 PORTDOCS= * .include diff --git a/science/ALPSCore/Makefile b/science/ALPSCore/Makefile index d4460f92ffd2..d6992a62de5d 100644 --- a/science/ALPSCore/Makefile +++ b/science/ALPSCore/Makefile @@ -1,56 +1,56 @@ PORTNAME= ALPSCore DISTVERSIONPREFIX= v DISTVERSION= 2.2.0 -PORTREVISION= 14 +PORTREVISION= 15 CATEGORIES= science MAINTAINER= ports@FreeBSD.org COMMENT= Generic algorithms and utilities for condensed matter physics LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE.TXT BROKEN_i386= fails to build: no matching member function for call to 'read' LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake compiler:c++11-lang eigen:3 USE_GITHUB= yes USE_LDCONFIG= yes TEST_TARGET= test # 2 to 3 tests fail: https://github.com/ALPSCore/ALPSCore/issues/388 CMAKE_ARGS+= -DTesting:BOOL=OFF # enable only for the 'test' target CMAKE_ARGS_TEST= -DTesting:BOOL=ON -DExtensiveTesting:BOOL=ON CXXFLAGS+= -DNDEBUG # see https://github.com/ALPSCore/ALPSCore/issues/389 LDFLAGS+= -lexecinfo # https://github.com/ALPSCore/ALPSCore/issues/390 OPTIONS_DEFINE= DOXYGEN DOCS OPENMPI OPTIONS_DEFAULT= OPENMPI DOXYGEN_IMPLIES= DOCS DOXYGEN_CMAKE_BOOL= Documentation DOXYGEN_BUILD_DEPENDS= doxygen:devel/doxygen OPENMPI_CMAKE_BOOL= ENABLE_MPI OPENMPI_LIB_DEPENDS= libmpi.so:net/openmpi PORTDOCS= * .include .if ${PORT_OPTIONS:MOPENMPI} CC= ${LOCALBASE}/mpi/openmpi/bin/mpicc CXX= ${LOCALBASE}/mpi/openmpi/bin/mpicxx .endif post-install-DOXYGEN-on: @${RM} ${STAGEDIR}${DOCSDIR}/.tag pre-test: @cd ${CONFIGURE_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} ${CMAKE_ARGS_TEST} ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} .include diff --git a/science/InsightToolkit/Makefile b/science/InsightToolkit/Makefile index 189e1931d920..419af12711c5 100644 --- a/science/InsightToolkit/Makefile +++ b/science/InsightToolkit/Makefile @@ -1,68 +1,68 @@ # Created by: bacon@smithers.neuro.mcw.edu PORTNAME= InsightToolkit PORTVERSION= 5.0.1 DISTVERSIONPREFIX=v -PORTREVISION= 7 +PORTREVISION= 8 CATEGORIES= science biology MASTER_SITES= https://github.com/InsightSoftwareConsortium/ITK/releases/download/v5.0.1/:data DISTFILES= InsightData-5.0.1.tar.gz:data MAINTAINER= ports@FreeBSD.org COMMENT= Insight Toolkit LICENSE= APACHE20 BUILD_DEPENDS= googletest>=0:devel/googletest LIB_DEPENDS= libgdcmCommon.so:devel/gdcm \ libexpat.so:textproc/expat2 \ libfftw.so:math/fftw \ libhdf5.so:science/hdf5 \ libpng.so:graphics/png \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libtiff.so:graphics/tiff USES= cmake compiler:c++11-lang eigen:3 jpeg pkgconfig USE_GITHUB= yes GH_ACCOUNT= InsightSoftwareConsortium GH_PROJECT= ITK CMAKE_ARGS+= -DBUILD_SHARED_LIBS:BOOL=ON \ -DITK_FORBID_DOWNLOADS:BOOL=ON \ -DITK_LEGACY_SILENT:BOOL=ON \ -DITK_USE_KWSTYLE:BOOL=OFF \ -DITK_USE_SYSTEM_EXPAT:BOOL=ON \ -DITK_USE_SYSTEM_FFTW:BOOL=ON \ -DITK_USE_SYSTEM_GDCM:BOOL=ON \ -DITK_USE_SYSTEM_HDF5:BOOL=ON \ -DITK_USE_SYSTEM_JPEG:BOOL=ON \ -DITK_USE_SYSTEM_LIBRARIES:BOOL=ON \ -DITK_USE_SYSTEM_PNG:BOOL=ON \ -DITK_USE_SYSTEM_TIFF:BOOL=ON \ -DITK_USE_SYSTEM_ZLIB:BOOL=ON \ -DModule_ITKIOMIC:BOOL=ON \ -DModule_ITKIOTransformMINC:BOOL=ON \ -DModule_ITKReview:BOOL=ON USE_LDCONFIG= ${PREFIX}/lib/InsightToolkit ITK_VER= ${PORTVERSION:R} PLIST_SUB+= ITK_VER=${ITK_VER} OPTIONS_DEFINE= EXAMPLES TESTING EXAMPLES_DESC= Build examples (very time consuming) TESTING_DESC= Build testing programs (very time consuming) EXAMPLES_CMAKE_ON= -DBUILD_EXAMPLES:BOOL=ON TESTING_CMAKE_ON= -DBUILD_TESTING:BOOL=ON .include .if ${CHOSEN_COMPILER_TYPE} == gcc PLIST_SUB+= CHOSEN_COMPILER_TYPE="GNU" .else PLIST_SUB+= CHOSEN_COMPILER_TYPE="Clang" .endif post-extract: ${MV} ${WRKDIR}/${PORTNAME}-${PORTVERSION}/.ExternalData/* ${WRKSRC}/.ExternalData/ ${RM} -r ${WRKDIR}/${PORTNAME}-${PORTVERSION} .include diff --git a/science/abinit/Makefile b/science/abinit/Makefile index 96b74303b2c3..49a68b01c2e0 100644 --- a/science/abinit/Makefile +++ b/science/abinit/Makefile @@ -1,96 +1,96 @@ # Created by: NAKATA Maho PORTNAME= abinit DISTVERSION= 9.4.2 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Full-featured atomic-scale first-principles simulation software LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le BUILD_DEPENDS= gm4:devel/m4 \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}pygments>=0:textproc/py-pygments@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}graphviz>0:graphics/py-graphviz@${PY_FLAVOR} LIB_DEPENDS= libelpa.so:math/elpa \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libelpa.so:math/elpa \ libxc.so:science/libxc \ libfftw3.so:math/fftw3 \ libhdf5.so:science/hdf5 \ libxml2.so:textproc/libxml2 \ libnetcdf.so:science/netcdf \ libxmlf90.so:textproc/xmlf90 \ libwannier.so:science/wannier90 \ libnetcdff.so:science/netcdf-fortran RUN_DEPENDS= atompaw:science/atompaw TEST_DEPENDS= ${PYNUMPY} \ libyaml>0:textproc/libyaml USES= autoreconf:build blaslapack:netlib fortran gmake gnome localbase:ldflags \ python:3.7+ shebangfix USE_GITHUB= yes USE_GNOME= libxml2 SHEBANG_FILES= config/scripts/* doc/tutorial/paral_gspw_assets/abinit.sub.* SHEBANG_GLOB= *.py GNU_CONFIGURE= yes CONFIGURE_ENV= CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}" \ LINALG_FCFLAGS="-I${LOCALBASE}/include/elpa-2019.05.002/modules" \ LINALG_LIBS="${BLASLIB} ${LAPACKLIB} -lelpa" \ NETCDF_FORTRAN_FCFLAGS=-I${LOCALBASE}/include \ XMLF90_FCFLAGS=-I${LOCALBASE}/include \ WANNIER90_LIBS="${BLASLIB} ${LAPACKLIB} -lwannier" CONFIGURE_ARGS= --with-fft --with-libxc --with-libxml2 --with-netcdf \ --with-netcdf-fortran --with-wannier90 --with-xmlf90 FCFLAGS+= -ffree-line-length-none TEST_TARGET= tests_abirules tests_buildsys TEST_WRKSRC= ${WRKSRC}/abichecks PORTDOCS= * OPTIONS_DEFINE= DOCS OPENMP MPI OPTIONS_DEFAULT= OPENMP MPI OPENMP_CONFIGURE_ENABLE= openmp OPENMP_LDFLAGS= -lomp MPI_CONFIGURE_WITH= mpi=yes # fftw3 not enabled because libfftw3_mpi is required but not packaged MPI_VARS= FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include \ CONFIGURE_ENV+=MPI_LIBS="`pkg-config --libs mpich` -lmpifort" \ CONFIGURE_ENV+MPI_LDFLAGS="`pkg-config --libs mpich` -lmpifort" MPI_BUILD_DEPENDS= mpich>0:net/mpich MPI_RUN_DEPENDS= mpich>0:net/mpich .if defined(WITH_LEVMAR) # --with-levmar seems deprecated LIB_DEPENDS+= liblevmar.so:math/levmar CONFIGURE_ENV+= LEVMAR_LIBS="-llevmar ${BLASLIB} ${LAPACKLIB}" CONFIGURE_ARGS+= --with-levmar .endif .include .if ${GCC_DEFAULT} >= 10 FCFLAGS+= -fallow-argument-mismatch # see https://github.com/abinit/abinit/issues/41 .endif pre-configure: (cd ${WRKSRC} && ./autogen.sh) post-install-DOCS-on: ${REINPLACE_CMD} -e 's|/usr/bin/env python|${PYTHON_CMD}|' \ ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py ${RM} ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py.bak @${MKDIR} ${STAGEDIR}${DOCSDIR} ${CP} -R ${WRKSRC}/doc/tutorial ${STAGEDIR}${DOCSDIR} pre-test: ${TOUCH} ${TEST_WRKSRC}/make.log .include diff --git a/science/ascent/Makefile b/science/ascent/Makefile index 65aeca47aeb2..77b6b2a0042f 100644 --- a/science/ascent/Makefile +++ b/science/ascent/Makefile @@ -1,37 +1,38 @@ PORTNAME= ascent DISTVERSIONPREFIX= v DISTVERSION= 0.8.0 +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= -visualizer MAINTAINER= yuri@FreeBSD.org COMMENT= Visualization and analysis runtime for multi-physics HPC simulations LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE LIB_DEPENDS= libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libsiloh5.so:science/silo \ libsysinfo.so:devel/libsysinfo \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake:testing compiler:c++11-lang fortran localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= Alpine-DAV GH_TUPLE= Alpine-DAV:spack_configs:26ea412:spack_configs/../scripts/uberenv_configs/spack_configs \ LLNL:blt:86a7d6b:blt/blt \ llnl:uberenv:105e384:uberenv/../scripts/uberenv CMAKE_OFF= ENABLE_PYTHON ENABLE_DOCS ENABLE_TESTS ENABLE_EXAMPLES CMAKE_OFF+= ENABLE_UTILS # utils are installed into a non-standard path, see https://github.com/Alpine-DAV/ascent/issues/814 CMAKE_OFF+= ENABLE_MPI # MPI fails to link, see https://github.com/Alpine-DAV/ascent/issues/813 CMAKE_ARGS= -DCONDUIT_DIR=${LOCALBASE} CMAKE_TESTING_ON= ENABLE_TESTS # one testcase fails because conduit lacks HDF5, see https://github.com/LLNL/conduit/issues/840 LDFLAGS+= -lsysinfo WRKSRC_SUBDIR= src .include diff --git a/science/avogadrolibs/Makefile b/science/avogadrolibs/Makefile index 37dad2dca8c0..fa146caa1036 100644 --- a/science/avogadrolibs/Makefile +++ b/science/avogadrolibs/Makefile @@ -1,70 +1,71 @@ PORTNAME= avogadrolibs DISTVERSION= 1.95.1 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Avogadro2 libraries for chemical editor and visualization applications LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE TEST_DEPENDS= googletest>0:devel/googletest USES= cmake:testing compiler:c++17-lang eigen:3,build,run # eigen needs to be 'run' because it is written into cmake files USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= OpenChemistry GH_TUPLE= OpenChemistry:molecules:b1e16c5:molecules/../molecules \ OpenChemistry:crystals:c3e2468:crystals/../crystals CMAKE_ON= BUILD_SHARED_LIBS CMAKE_TESTING_ON= ENABLE_TESTING OPTIONS_DEFINE= HDF5 LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB VTK OPTIONS_DEFAULT= LIBARCHIVE LIBMSYM MMTF OPENGL QT5 SPGLIB OPTIONS_SUB= yes HDF5_CMAKE_BOOL= USE_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec LIBARCHIVE_DESC= Enable optional Libarchive features LIBARCHIVE_CMAKE_BOOL= USE_LIBARCHIVE LIBARCHIVE_USES= libarchive LIBARCHIVE_IMPLIES= QT5 LIBMSYM_DESC= Enable optional features using libmsym LIBMSYM_CMAKE_BOOL= USE_LIBMSYM LIBMSYM_LIB_DEPENDS= libmsym.so:science/libmsym LIBMSYM_IMPLIES= QT5 # enables the 'symmetry' Qt plugin MMTF_DESC= Enable optional features using mmtf MMTF_CMAKE_BOOL= USE_MMTF MMTF_BUILD_DEPENDS= mmtf-cpp>0:science/mmtf-cpp OPENGL_CMAKE_BOOL= USE_OPENGL OPENGL_USES= gl OPENGL_USE= GL=gl,glew,glu QT5_CMAKE_BOOL= USE_QT QT5_USES= qt:5 QT5_USE= QT=core,concurrent,gui,network,svg,widgets,buildtools_build,qmake_build QT5_IMPLIES= OPENGL SPGLIB_DESC= Enable optional features using spglib SPGLIB_CMAKE_BOOL= USE_SPGLIB SPGLIB_CMAKE_ON= -DSPGLIB_INCLUDE_DIR=${LOCALBASE}/include/spglib SPGLIB_LIB_DEPENDS= libsymspg.so:science/spglib SPGLIB_IMPLIES= QT5 # USE_SPGLIB only installs header file without USE_QT, and also installs SpaceGroup.a with USE_QT, see https://github.com/OpenChemistry/avogadrolibs/issues/610 VTK_DESC= Enable libraries that use VTK VTK_CMAKE_BOOL= USE_VTK VTK_LIB_DEPENDS= libvtksys-8.2.so:math/vtk8 VTK_IMPLIES= QT5 VTK_BROKEN= Needs https://github.com/psavery/genXrdPattern, etc post-install: @${RM} -r ${STAGEDIR}${PREFIX}/share/doc .include diff --git a/science/axom/Makefile b/science/axom/Makefile index 250a27ae4001..8792a4fa1a93 100644 --- a/science/axom/Makefile +++ b/science/axom/Makefile @@ -1,49 +1,50 @@ PORTNAME= axom DISTVERSIONPREFIX= v DISTVERSION= 0.6.1 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Infrastructure for development of multi-physics applications and tools LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE BROKEN_i386= https://github.com/LLNL/axom/issues/743 BROKEN_powerpc= https://github.com/LLNL/axom/issues/743 LIB_DEPENDS= libconduit.so:science/conduit \ libhdf5.so:science/hdf5 \ libsiloh5.so:science/silo \ - libsz.so:science/szip + libsz.so:science/libaec RUN_DEPENDS= sparsehash>0:devel/sparsehash USES= cmake compiler:c++11-lang USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= LLNL:axom_data:b3d8e6f:axom_data/../data \ LLNL:blt:ddd5a0c:blt/cmake/blt \ LLNL:uberenv:a121a45:uberenv/scripts/uberenv CMAKE_OFF= AXOM_ENABLE_DOCS AXOM_ENABLE_EXAMPLES AXOM_ENABLE_TESTS FREEBSD_ENABLE_EXAMPLES CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DCONDUIT_DIR=${LOCALBASE} \ -DHDF5_DIR=${LOCALBASE} LDFLAGS+= -lexecinfo WRKSRC_SUBDIR= src CONFLICTS_INSTALL= libfmt # bundles and installs an incompatible libfmt version: https://github.com/LLNL/axom/issues/561, axom headers include fmt unnecessarily post-install: # installs headers of a third party library sparsehash: https://github.com/LLNL/axom/issues/365 @${RM} -r ${STAGEDIR}${PREFIX}/include/sparsehash do-test: @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DAXOM_ENABLE_TESTS:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include diff --git a/science/cdo/Makefile b/science/cdo/Makefile index 15444dd2dfa7..da2a1f823586 100644 --- a/science/cdo/Makefile +++ b/science/cdo/Makefile @@ -1,80 +1,81 @@ # Created by: Sunpoet Po-Chuan Hsieh PORTNAME= cdo PORTVERSION= 2.0.5 +PORTREVISION= 1 CATEGORIES= science MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/26823/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Climate Data Operators LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING OPTIONS_DEFINE= CGRIBEX ECCODES HDF5 JASPER NETCDF PROJ SZIP UDUNITS UUID OPTIONS_DEFAULT=CGRIBEX ECCODES HDF5 JASPER NETCDF PROJ SZIP UDUNITS UUID OPTIONS_SUB= yes CGRIBEX_DESC= Use CGRIBEX library for GRIB1 files ECCODES_DESC= Use ecCodes for GRIB files HDF5_IMPLIES= SZIP NETCDF_IMPLIES= HDF5 UUID_DESC= UUID support PORTSCOUT= site:https://code.mpimet.mpg.de/projects/cdo/files USES= compiler:c++14-lang gmake libtool localbase pathfix CONFIGURE_ARGS= --disable-data \ --disable-extra \ --disable-fortran \ --disable-ieg \ --disable-openmp \ --disable-service \ --enable-cdi-lib \ --program-transform-name="" \ --with-zlib=/usr GNU_CONFIGURE= yes INSTALL_TARGET= install-strip MAKE_JOBS_UNSAFE= yes TEST_TARGET= check USE_CXXSTD= c++14 USE_LDCONFIG= yes CGRIBEX_CONFIGURE_WITH= cgribex CGRIBEX_LIB_DEPENDS= libcgribex.so:science/cgribex ECCODES_CONFIGURE_WITH= eccodes ECCODES_LIB_DEPENDS= libeccodes.so:science/eccodes HDF5_CONFIGURE_WITH= hdf5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 JASPER_CONFIGURE_WITH= jasper JASPER_LIB_DEPENDS= libjasper.so:graphics/jasper NETCDF_CONFIGURE_WITH= netcdf NETCDF_LIB_DEPENDS= libnetcdf.so:science/netcdf PROJ_CONFIGURE_WITH= proj PROJ_LIB_DEPENDS= libproj.so:graphics/proj SZIP_CONFIGURE_WITH= szlib -SZIP_LIB_DEPENDS= libsz.so:science/szip +SZIP_LIB_DEPENDS= libsz.so:science/libaec UDUNITS_CONFIGURE_WITH= udunits2 UDUNITS_LIB_DEPENDS= libudunits2.so:science/udunits UUID_CONFIGURE_OFF= ac_cv_func_uuid_create=no ac_cv_have_decl_uuid_create=no ac_cv_have_decl_uuid_generate=no ac_cv_lib_uuid_uuid_generate=no UUID_LIB_DEPENDS= libuuid.so:misc/e2fsprogs-libuuid .include .if ${ARCH} != "sparc64" CFLAGS+= -DPTHREAD_MUTEXATTR .endif post-patch: @${REINPLACE_CMD} -e '/^SUBDIRS = / s| contrib||' ${WRKSRC}/Makefile.in @${REINPLACE_CMD} -e 's|$$(libdir)/\($$$$pkgconfigfile\)|${PREFIX}/libdata/\1|' ${WRKSRC}/libcdi/src/Makefile.in @${REINPLACE_CMD} -e 's|unsigned32 |uint32_t |' ${WRKSRC}/libcdi/src/cdilib.c ${WRKSRC}/libcdi/src/util.c post-install: ${INSTALL_DATA} ${WRKSRC}/libcdi/src/cdi.inc ${STAGEDIR}${PREFIX}/include/cdi.inc test-NETCDF-on: @cd ${WRKSRC}/ && ${SETENV} CDO_PATH=src/cdo src/cdotest .include diff --git a/science/cgnslib/Makefile b/science/cgnslib/Makefile index 0611a1aff8d5..0b1d574c80d8 100644 --- a/science/cgnslib/Makefile +++ b/science/cgnslib/Makefile @@ -1,63 +1,65 @@ # Created by: thierry@pompo.net PORTNAME= cgnslib PORTVERSION= 4.3.0 DISTVERSIONPREFIX= v +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= science MAINTAINER= thierry@FreeBSD.org COMMENT= CFD General Notation System library code LICENSE= AS-IS LICENSE_NAME= AS-IS LICENSE_FILE= ${WRKSRC}/license.txt LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept USES= cmake USE_GITHUB= yes GH_ACCOUNT= CGNS GH_PROJECT= CGNS USE_LDCONFIG= yes MAKE_JOBS_UNSAFE= yes #CMAKE_ARGS= -DOpenGL_GL_PREFERENCE:STRING="GLVND" CMAKE_ARGS= -DOpenGL_GL_PREFERENCE:STRING="LEGACY" FFLAGS+= -fPIC -std=legacy TEST_TARGET= test OPTIONS_DEFINE= FORTRAN HDF5 TESTS TOOLS OPTIONS_DEFAULT= FORTRAN HDF5 TESTS TOOLS OPTIONS_SUB= yes HDF5_DESC= Enable HDF5 interface TESTS_DESC= Enable test programs TOOLS_DESC= Build the CGNSTools package FORTRAN_USES= fortran FORTRAN_CMAKE_BOOL= CGNS_ENABLE_FORTRAN -HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 libsz.so:science/szip +HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 \ + libsz.so:science/libaec HDF5_CMAKE_BOOL= CGNS_ENABLE_HDF5 HDF5_CMAKE_ON= -DHDF5_INCLUDE_PATH:PATH="${LOCALBASE}/include" TESTS_CMAKE_BOOL= CGNS_ENABLE_TESTS TOOLS_USES= gl localbase tk xorg TOOLS_LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 TOOLS_USE= GL=egl,gl,glu \ XORG=ice,sm,x11,xau,xcomposite,xcursor,xdamage,xdmcp,xext,xfixes,xft,xi,xinerama,xkbfile,xmu,xpm,xrandr,xrender,xres,xscrnsaver,xt,xtst,xv,xxf86vm TOOLS_CMAKE_BOOL= CGNS_BUILD_CGNSTOOLS TOOLS_CMAKE_ON= -DTCL_INCLUDE_PATH:STRING="${TCL_INCLUDEDIR}" \ -DTK_INCLUDE_PATH:STRING="${TK_INCLUDEDIR}" post-install: ${RLN} ${STAGEDIR}${PREFIX}/lib/libcgns.so.${PORTVERSION:R} \ ${STAGEDIR}${PREFIX}/lib/libcgns.so.${PORTVERSION:R:R} do-test: cd ${TEST_WRKSRC} && \ ${SETENV} ${TEST_ENV} ctest -C ${CMAKE_BUILD_TYPE} .include diff --git a/science/cgribex/Makefile b/science/cgribex/Makefile index 3cd45742337a..dedba8523f3e 100644 --- a/science/cgribex/Makefile +++ b/science/cgribex/Makefile @@ -1,39 +1,39 @@ # Created by: Sunpoet Po-Chuan Hsieh PORTNAME= cgribex PORTVERSION= 1.9.4 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://code.mpimet.mpg.de/attachments/download/21178/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Lightweight GRIBEX in C with portable Fortran interface LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING USES= libtool CPPFLAGS+= -DgFortran GNU_CONFIGURE= yes INSTALL_TARGET= install-strip USE_LDCONFIG= yes OPTIONS_DEFINE= GRIB_API JASPER SZIP OPTIONS_DEFAULT=JASPER SZIP GRIB_API_CONFIGURE_WITH=grib_api=${LOCALBASE} GRIB_API_LIB_DEPENDS= libgrib_api.so:science/grib_api JASPER_CONFIGURE_WITH= jasper=${LOCALBASE} JASPER_LIB_DEPENDS= libjasper.so:graphics/jasper SZIP_CONFIGURE_WITH= szlib=${LOCALBASE} -SZIP_LIB_DEPENDS= libsz.so:science/szip +SZIP_LIB_DEPENDS= libsz.so:science/libaec post-configure: @${REINPLACE_CMD} -e 's|-Ino/include||g; s|-Lno/lib||g' ${WRKSRC}/Makefile ${WRKSRC}/*/Makefile post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libcgribex.so .include diff --git a/science/chemps2/Makefile b/science/chemps2/Makefile index cbd79e8e0565..4fea31cc72cb 100644 --- a/science/chemps2/Makefile +++ b/science/chemps2/Makefile @@ -1,27 +1,28 @@ PORTNAME= CheMPS2 DISTVERSIONPREFIX= v DISTVERSION= 1.8.12 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Spin-adapted implementation of DMRG for ab initio quantum chemistry LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec USES= blaslapack:openblas cmake fortran USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= SebWouters CMAKE_ARGS+= -DSHARED_ONLY:BOOL=ON CMAKE_ARGS+= -DENABLE_TESTS:BOOL=OFF CMAKE_ARGS+= -DENABLE_XHOST:BOOL=OFF # shouldn't optimize the port in case of central build CMAKE_ARGS+= -DENABLE_OPENMP:BOOL=OFF # find_package(OpenMP) is broken since the merge into cmake: bug#223678 CMAKE_ARGS+= -DLAPACK_LIBRARIES="-lopenblas" # can't find it using find_package for some reason .include diff --git a/science/chrono/Makefile b/science/chrono/Makefile index 42b206a2f53c..6c46d90fc27a 100644 --- a/science/chrono/Makefile +++ b/science/chrono/Makefile @@ -1,123 +1,123 @@ PORTNAME= chrono DISTVERSION= 7.0.3 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science devel PKGNAMESUFFIX= -physics-simulation-engine PATCH_SITES= https://github.com/${GH_ACCOUNT}/${GH_PROJECT}/commit/ PATCHFILES= 74df5c76d8d475818138a9a16ceccbd6f326247c.patch:-p1 # https://github.com/projectchrono/chrono/pull/295 MAINTAINER= yuri@FreeBSD.org COMMENT= C++ library for multi-physics simulation LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= use of overloaded operator '[]' is ambiguous (with operand types 'chrono::quaternion' and 'int'): https://github.com/projectchrono/chrono/issues/158 BROKEN_aarch64= cannot find -lFALSE, see https://github.com/projectchrono/chrono/issues/389 BUILD_DEPENDS= openmpi>0:net/openmpi LIB_DEPENDS= libblas.so:math/blas \ libepoll-shim.so:devel/libepoll-shim \ libfabric.so:net/libfabric \ libhwloc.so:devel/hwloc2 \ libjson-c.so:devel/json-c \ libmetis.so:math/metis \ libpciaccess.so:devel/libpciaccess \ libpng16.so:graphics/png \ libscotch.so:cad/scotch \ libze_loader.so:devel/level-zero USES= cmake compiler:c++14-lang eigen:3 fortran gnome jpeg xorg USE_LDCONFIG= yes USE_GNOME= libxml2 USE_XORG= x11 xau xcb xdmcp xext xxf86vm USE_GITHUB= yes GH_ACCOUNT= project${PORTNAME} ALL_MODULES= Cascade Cosimulation Distributed FSI Irrlicht Multicore MUMPS OpenGL Pardiso_Project Postprocess Sensor SynChrono Vehicle # module names in a human readable case; for the list of available modules: grep -r "option(ENABLE_MODULE" work OPTIONS_DEFINE= HDF5 DEMOS OPTIONS_GROUP= MODULES OPTIONS_GROUP_MODULES= ${ALL_MODULES:tu} MODULES_DESC= Enable modules: OPTIONS_DEFAULT= HDF5 OPTIONS_SUB= yes HDF5_CMAKE_BOOL= ENABLE_HDF5 HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 DEMOS_DESC= Build and install demo programs DEMOS_CMAKE_BOOL= BUILD_DEMOS DEMOS_BROKEN= /usr/local/lib/libdmumps.so: undefined reference to `mpi_pack_' CASCADE_CMAKE_ON= -DCASCADE_INCLUDE_DIR:STRING=${LOCALBASE}/include/OpenCASCADE -DCASCADE_LIBDIR:STRING=${LOCALBASE}/lib CASCADE_LIB_DEPENDS= libTKernel.so:cad/opencascade740 DISTRIBUTED_BROKEN= requires cuda_runtime_api.h in thrust package which is missing for some reason DISTRIBUTED_IMPLIES= MULTICORE FSI_BROKEN= requires CUDA IRRLICHT_LIB_DEPENDS= libIrrlicht.so:x11-toolkits/irrlicht MULTICORE_BUILD_DEPENDS= blaze>0:math/blaze \ thrust>0:devel/thrust MUMPS_CMAKE_ON= -DMUMPS_ROOT:STRING=${LOCALBASE} MUMPS_LIB_DEPENDS= libdmumps.so:math/mumps \ libopenblas.so:math/openblas PARDISO_PROJECT_BROKEN= Not available for FreeBSD; License is restrictive SENSOR_BROKEN= requires CUDA SYNCHRONO_USES= localbase SYNCHRONO_BUILD_DEPENDS= flatc:devel/flatbuffers205 # until https://github.com/projectchrono/chrono/issues/391 is fixed SYNCHRONO_LIB_DEPENDS= libmpi.so:net/mpich SYNCHRONO_IMPLIES= VEHICLE OPENGL_USES= gl OPENGL_USE= GL=gl,glu,glew OPENGL_BUILD_DEPENDS= ${LOCALBASE}/include/glm/glm.hpp:math/glm OPENGL_LIB_DEPENDS= libglfw.so:graphics/glfw -VEHICLE_LIB_DEPENDS= libsz.so:science/szip \ +VEHICLE_LIB_DEPENDS= libsz.so:science/libaec \ libmpi.so:net/openmpi .for module in ${ALL_MODULES} ${module:tu}_DESC= Chrono ${module} module ${module:tu}_CMAKE_BOOL= ENABLE_MODULE_${module:tu} .if "${${module:tu}_BROKEN}" == "" OPTIONS_DEFAULT+= ${module:tu} .endif .endfor #.include .include .if ${PORT_OPTIONS:MVEHICLE} && ${PORT_OPTIONS:MIRRLICHT} PLIST_FILES+= lib/libChronoEngine_vehicle_irrlicht.so .endif #.include .if ${CHOSEN_COMPILER_TYPE} == gcc CXXFLAGS+= -Wno-error=narrowing .endif post-extract: @${RM} ${WRKSRC}/data/opensim/Rajagopal2015.orig post-patch: @${FIND} ${WRKSRC} -name CMakeLists.txt -o -name "*.cmake*" | ${XARGS} ${REINPLACE_CMD} -i '' 's|lib64|lib|' do-test: @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DBUILD_TESTING:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ctest -C ${CMAKE_BUILD_TYPE} ${_MAKE_JOBS} .include diff --git a/science/conduit/Makefile b/science/conduit/Makefile index baeadd0dc9d4..c49627744622 100644 --- a/science/conduit/Makefile +++ b/science/conduit/Makefile @@ -1,36 +1,37 @@ PORTNAME= conduit DISTVERSIONPREFIX= v DISTVERSION= 0.8.3 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Simplified data exchange for HPC simulations LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/../LICENSE LIB_DEPENDS= libhdf5.so:science/hdf5 \ libmpi_cxx.so:net/openmpi \ libsiloh5.so:science/silo \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake:testing compiler:c++11-lang fortran USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= LLNL GH_TUPLE= LLNL:blt:86a7d6b:blt/blt \ Alpine-DAV:spack_configs:85f7382:spack_configs/../scripts/uberenv_configs/spack_configs \ LLNL:uberenv:105e384:LLNL_uberenv/../scripts/uberenv WRKSRC_SUBDIR= src CMAKE_ON= ENABLE_FORTRAN ENABLE_MPI CMAKE_OFF= CONDUIT_ENABLE_TESTS ENABLE_DOCS ENABLE_EXAMPLES ENABLE_GIT ENABLE_TESTS ENABLE_VALGRIND CMAKE_ARGS= -DHDF5_DIR=${LOCALBASE} \ -DSILO_DIR=${LOCALBASE} \ -DFREEBSD_EXAMPLESDIR=${EXAMPLESDIR} # complete list of optional dependencies (enabled with *_DIR): https://llnl-conduit.readthedocs.io/en/latest/building.html #CMAKE_ARGS+= -DADIOS_DIR=${LOCALBASE} # broken, see https://github.com/LLNL/conduit/issues/841 CMAKE_TESTING_ON= ENABLE_TESTS .include diff --git a/science/dakota/Makefile b/science/dakota/Makefile index 50520aba8696..824252641ab1 100644 --- a/science/dakota/Makefile +++ b/science/dakota/Makefile @@ -1,93 +1,93 @@ PORTNAME= dakota DISTVERSION= 6.15.0 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= https://dakota.sandia.gov/sites/default/files/distributions/public/ DISTNAME= ${PORTNAME}-${DISTVERSION}-public-src-cli DISTFILES= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Interface between analysis codes & iterative systems analysis methods LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= nanoflann>0:math/nanoflann LIB_DEPENDS= libblas.so:math/blas \ libboost_system.so:devel/boost-libs \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ liblapack.so:math/lapack \ libnlopt.so:math/nlopt \ - libsz.so:science/szip + libsz.so:science/libaec RUN_DEPENDS= bash:shells/bash USES= cmake compiler:c++11-lang fortran motif perl5 pkgconfig python shebangfix xorg USE_XORG= ice sm x11 xau xdmcp xext xft xmu xrender xt USE_LDCONFIG= yes USE_GITHUB= nodefault GH_TUPLE= stan-dev:math:v2.18.0:stanmath/stanmath SHEBANG_GLOB= *.sh *.py SHEBANG_FILES= interfaces/Python/mpitile \ scripts/pyprepro/dprepro \ scripts/pyprepro/pyprepro \ scripts/dprepro.perl \ test/dakota_test.perl CMAKE_ON= HAVE_X_GRAPHICS # always enable graphics because w/out it a lot of unrelated files aren't installed due to bugs in the project CMAKE_ON+= Boost_NO_BOOST_CMAKE \ DAKOTA_GIT_checkout #CMAKE_ON+= HAVE_C3 # causes "duplicate include" error #CMAKE_ON+= DAKOTA_DL_SOLVER # fails to compile: error: declaration of anonymous class must be a definition #CMAKE_ON+= HAVE_NOWPAC # installs files into $PORTSDIR CMAKE_ON+= HAVE_QUESO \ HAVE_MUQ MUQ_USE_PYTHON \ # enable some methods that aren't enabled by default, see the list @ src/DakotaIterator.cpp CMAKE_ON+= DAKOTA_HAVE_GSL DAKOTA_HAVE_HDF5 CMAKE_OFF= DAKOTA_ENABLE_TESTS CMAKE_ARGS= -DDakota_VERSION_SRC:STRING=${DISTVERSION} -DDakota_GIT_REVL:STRING=unknown -DDakota_RELEASE_DATE:${STRING}=20211115 \ -DPython_EXECUTABLE=${PYTHON_CMD} \ -DMUQ_STANMATH_DIR=${WRKSRC}/stanmath FFLAGS+= -fallow-argument-mismatch LDFLAGS+= -lexecinfo CONFLICTS_BUILD= dakota # self: picks up some bundled packages from the pre-installed dakota package and then fails to install them CONFLICTS_INSTALL= openblas post-extract: @${FIND} ${WRKSRC} -name "*.orig" -delete @${ECHO} ${DISTVERSION} > ${WRKSRC}/VERSION # expected by the 'install' target pre-configure: # MUQ_STANMATH_DIR is lost otherwise @${REINPLACE_CMD} 's|find_package(PkgConfig)|set(MUQ_STANMATH_DIR ${WRKSRC}/stanmath)|' ${WRKSRC}/packages/external/muq2/cmake/finds/FindSTANMATH.cmake post-install: # remove eigen3 that Dakota installs cd ${STAGEDIR}${PREFIX} && ${RM} -r include/eigen3 share/eigen3 # remove cblas.h that Dakota installs ${RM} ${STAGEDIR}${PREFIX}/include/cblas.h # remove *.orig files ${RM} ${STAGEDIR}${PREFIX}/include/colin/AppResponse.h.orig # install libraries that it fails to install .for l in libmuqSamplingAlgorithms.so libmuqApproximation.so libmuqInference.so libmuqModeling.so libmuqOptimization.so libmuqUtilities.so ${INSTALL_LIB} ${BUILD_WRKSRC}/packages/external/muq2/lib/${l} ${STAGEDIR}${PREFIX}/lib .endfor do-test: # from Additional Test Suites @ https://dakota.sandia.gov/content/additional-test-suites (many tests are known to fail) ## minimal set of fast-running tests that should NOT FAIL (may DIFF, depending on platform / compiler) #cd ${WRKSRC}/test && ./dakota_test.perl ## test suite that should PASS on any supported platform (NO DIFF or FAIL) #cd ${WRKSRC}/test && ./dakota_test.perl --label-regex=AcceptanceTest ## run all Dakota tests active in this build (should PASS or DIFF) #cd ${WRKSRC}/test && ./dakota_test.perl --label-regex=dakota_ # Tests should be this way, but this fails: @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DDAKOTA_ENABLE_TESTS:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ (cd ${WRKSRC} && ctest -j 4 -L FastTest -LE Diff) .include diff --git a/science/dynare/Makefile b/science/dynare/Makefile index 59e21deada34..b004eddfb238 100644 --- a/science/dynare/Makefile +++ b/science/dynare/Makefile @@ -1,55 +1,56 @@ PORTNAME= dynare DISTVERSION= 5.1 +PORTREVISION= 1 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 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= ${LOCALBASE}/include/boost/tokenizer.hpp:devel/boost-libs LIB_DEPENDS= libhdf5.so:science/hdf5 \ libmatio.so:math/matio \ libopenblas.so:math/openblas \ - libsz.so:science/szip + libsz.so:science/libaec RUN_DEPENDS= epstool:graphics/epstool \ gnuplot:math/gnuplot \ pstoedit:graphics/pstoedit \ xfig:graphics/xfig # README says that these executables are required for the test suite USES= bison compiler:c++17-lang fortran gmake localbase tar:xz USE_TEX= pdftex USE_GCC= yes # clang-11 fails: error: reference to local binding 'ii1' declared in enclosing function 'ss2Iteration_pruning' # Clang still doesn't support this c++20 feature, see https://bugs.llvm.org/show_bug.cgi?id=49238 GNU_CONFIGURE= yes CONFIGURE_ARGS= --disable-matlab \ --disable-doc FCFLAGS+= -fPIC # required because configure tests with -shared SUB_FILES= pkg-message OPTIONS_DEFINE= OCTAVE OPTIONS_DEFAULT= OCTAVE OPTIONS_SUB= yes OCTAVE_DESC= Integrate with Octave (main way to use Dynare) OCTAVE_CONFIGURE_ENABLE= octave OCTAVE_CONFIGURE_ON= --disable-mex-kalman-steady-state # Kalman Steady State MEX file for Octave - requires the non-free library slicot-5.0 OCTAVE_BUILD_DEPENDS= octave:math/octave OCTAVE_LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float \ libgsl.so:math/gsl \ libumfpack.so:math/suitesparse-umfpack OCTAVE_RUN_DEPENDS= octave:math/octave post-install: # remove empty directories, see https://git.dynare.org/Dynare/dynare/-/issues/1835 @${FIND} ${STAGEDIR}${PREFIX} -type d -empty -delete .include diff --git a/science/erkale/Makefile b/science/erkale/Makefile index 1638baadf1d4..8555996330c5 100644 --- a/science/erkale/Makefile +++ b/science/erkale/Makefile @@ -1,67 +1,68 @@ PORTNAME= erkale DISTVERSION= g20220405 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry program to solve the electronic structure of atoms LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BROKEN_i386= liberkale_omp.so.0.1.0: undefined reference to `__atomic_compare_exchange' BUILD_DEPENDS= armadillo>0:math/armadillo LIB_DEPENDS= libderiv.so:science/libint \ libgsl.so:math/gsl \ libhdf5.so:science/hdf5 \ libint.so:science/libint \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libxc.so:science/libxc RUN_DEPENDS= ${LOCALBASE}/share/erkale/basis/6-21G.gbs:science/erkale-pseudopotentials FLAVORS= parallel serial FLAVOR?= ${FLAVORS:[1]} serial_PKGNAMESUFFIX= -serial USES= cmake:noninja compiler:c11 fortran pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= susilehtola GH_TAGNAME= f005a9ed588d7b6fcda54648db16523419308cbd TEST_TARGET= test CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DERKALE_SYSTEM_LIBRARY=${DATADIR}/basis PLIST_SUB= SUFFIX="${SUFFIX}" .if ${FLAVOR} == serial CMAKE_OFF= USE_OPENMP .else # parallel CMAKE_ON+= USE_OPENMP SUFFIX= _omp .endif OPTIONS_SINGLE= LINALG OPTIONS_SINGLE_LINALG= NETLIB OPENBLAS OPTIONS_DEFAULT= OPENBLAS LINALG_DESC= Linear algebra library NETLIB_USES= blaslapack:netlib NETLIB_CMAKE_ON= -DLAPACK_LIBRARIES:STRING=-llapack -DBLAS_LIBRARIES:STRING=-lblas NETLIB_LDFLAGS= ${LOCALBASE}/lib/libcblas.so ${LOCALBASE}/lib/liblapack.so ${LOCALBASE}/lib/libblas.so NETLIB_LIB_DEPENDS= libcblas.so:math/cblas NETLIB_BROKEN= choosing NETLIB causes a conflict: openblas-0.3.7_3,1 conflicts with cblas-1.0_12 on /usr/local/include/cblas.h OPENBLAS_USES= blaslapack:openblas OPENBLAS_CMAKE_ON= -DLAPACK_LIBRARIES:STRING=-lopenblas -DBLAS_LIBRARIES:STRING=-lopenblas .if ${FLAVOR} == parallel post-install: @${MV} ${STAGEDIR}${PREFIX}/include/erkale ${STAGEDIR}${PREFIX}/include/erkale${SUFFIX} @${MV} ${STAGEDIR}${PREFIX}/bin/erkale_bastool ${STAGEDIR}${PREFIX}/bin/erkale_bastool${SUFFIX} .endif .include diff --git a/science/gnudatalanguage/Makefile b/science/gnudatalanguage/Makefile index 38089180b737..1be2972fbe74 100644 --- a/science/gnudatalanguage/Makefile +++ b/science/gnudatalanguage/Makefile @@ -1,154 +1,154 @@ # Created by: thierry@pompo.net PORTNAME= gnudatalanguage PORTVERSION= 1.0.1 DISTVERSIONPREFIX= v -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science lang .if defined(BUILD_PYTHON_MODULE) PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} .endif MAINTAINER= thierry@FreeBSD.org COMMENT?= Free IDL-compatible incremental compiler LICENSE= GPLv2 LIB_DEPENDS+= libgeotiff.so:graphics/libgeotiff\ libexpat.so:textproc/expat2 \ libplplot.so:math/plplot \ libtiff.so:graphics/tiff \ libshp.so:devel/shapelib \ libpng.so:graphics/png \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libps.so:print/pslib \ libgsl.so:math/gsl USE_GITHUB= yes GH_PROJECT= gdl USES= cmake compiler:c++11-lang fortran ncurses pkgconfig readline \ xorg USE_WX= 3.0+ USE_XORG= x11 sm ice xext # Disable ncurses and readline from ports # TODO: create a port for Astron http://idlastro.gsfc.nasa.gov/ftp/astron.tar.gz # TODO: create a port for TexToIdl http://physics.mnstate.edu/mcraig/textoidl/textoidl-2-1-2.tar CMAKE_ARGS= -DREADLINEDIR:STRING="/usr" \ -DOPENMP:BOOL=ON \ -DNCURSESDIR:STRING="/usr" \ -DPYTHON:BOOL=NO CPPFLAGS+= ${CFLAGS} -fno-inline -DNPY_NO_DEPRECATED_API -DNPY_1_7_API_VERSION CXXFLAGS+= -std=gnu++11 LDFLAGS+= -lpthread -L${LOCALBASE}/lib TEST_TARGET= test SLAVEDIRS= science/py-gnudatalanguage # Upstream prefer GraphicsMagick over ImageMackick # see https://github.com/gnudatalanguage/gdl/issues/611 # and https://github.com/gnudatalanguage/gdl/issues/1044 for ImageMagick 7 OPTIONS_DEFINE= EIGEN EXAMPLES FFTW GLPK GRAPHICSMAGICK GRIB HDF5 LIBPROJ4 MPI NETCDF PYTHON UDUNITS OPTIONS_DEFAULT=EIGEN FFTW GLPK GRAPHICSMAGICK GRIB HDF5 LIBPROJ4 NETCDF PYTHON UDUNITS EIGEN_DESC= Eigen3 support (boost performance) EIGEN_USES= eigen:3 EIGEN_CMAKE_ON= -DEIGEN3:BOOL=YES EIGEN_CMAKE_OFF= -DEIGEN3:BOOL=NO FFTW_LIB_DEPENDS= libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float FFTW_CMAKE_ON= -DFFTW:BOOL=YES FFTW_CMAKE_OFF= -DFFTW:BOOL=NO GLPK_DESC= Support GLPK for Simplex (Linear programming) GLPK_LIB_DEPENDS= libglpk.so:math/glpk GLPK_CMAKE_ON= -DGLPK=ON:BOOL=YES GLPK_CMAKE_OFF= -DGLPK=OFF:BOOL=NO GRAPHICSMAGICK_DESC= Support GraphicsMagick GRAPHICSMAGICK_LIB_DEPENDS= libGraphicsMagick.so:graphics/GraphicsMagick GRAPHICSMAGICK_CMAKE_ON= -DGRAPHICSMAGICK:BOOL=YES GRAPHICSMAGICK_CMAKE_OFF= -DGRAPHICSMAGICK:BOOL=NO # Temporary swith to ImageMagick #IMAGEMAGICK_DESC= Support ImageMagick #IMAGEMAGICK_LIB_DEPENDS=libMagick++-7.so:graphics/ImageMagick7 #IMAGEMAGICK_CMAKE_ON= -DGRAPHICSMAGICK:BOOL=NO -DMAGICK:BOOL=YES -DMAGICKDIR=${LOCALBASE} #IMAGEMAGICK_CMAKE_OFF= -DMAGICK:BOOL=NO GRIB_DESC= Support GRIB messages GRIB_LIB_DEPENDS= libeccodes.so:science/eccodes GRIB_CMAKE_ON= -DGRIB:BOOL=YES GRIB_CMAKE_OFF= -DGRIB:BOOL=NO HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 HDF5_CMAKE_ON= -DHDF5:BOOL=YES HDF5_CMAKE_OFF= -DHDF5:BOOL=NO -DHDF:BOOL=NO LIBPROJ4_DESC= Support cartographic processes LIBPROJ4_LIB_DEPENDS= libproj.so:graphics/proj LIBPROJ4_CMAKE_ON= -DLIBPROJ:BOOL=YES LIBPROJ4_CMAKE_OFF= -DLIBPROJ:BOOL=NO MPI_LIB_DEPENDS= libmpich.so:net/mpich MPI_CMAKE_ON= -DMPI:BOOL=ON MPI_CMAKE_OFF= -DMPI:BOOL=OFF -DMPIDIR=/none NETCDF_LIB_DEPENDS= libnetcdf.so:science/netcdf NETCDF_CMAKE_ON= -DNETCDF:BOOL=YES -DHDF:BOOL=NO NETCDF_CMAKE_OFF= -DNETCDF:BOOL=NO PYTHON_USES= python:3.7+ PYTHON_BUILD_DEPENDS= ${PYNUMPY} PYTHON_RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} PYTHON_CMAKE_ON= -DPYTHON:BOOL=YES -DPYTHONVERSION:STRING="${PYTHON_VER}" PYTHON_CMAKE_OFF= -DPYTHON:BOOL=NO # QHULL IS NOT NEEDED YET! #QHULL_DESC= Enable Triangulate and Qhull support #QHULL_LIB_DEPENDS= libqhull.so:math/qhull #QHULL_CMAKE_ON= -DQHULL:BOOL=YES #QHULL_CMAKE_OFF= -DQHULL:BOOL=NO UDUNITS_LIB_DEPENDS= libudunits2.so:science/udunits UDUNITS_CMAKE_ON= -DUDUNITS2:BOOL=YES UDUNITS_CMAKE_OFF= -DUDUNITS2:BOOL=NO .if defined(BUILD_PYTHON_MODULE) CATEGORIES+= python CMAKE_ARGS+= -DPYTHON_MODULE:BOOL=YES PLIST= ${.CURDIR}/pkg-plist.pymod .else CMAKE_ARGS+= -DPYTHON_MODULE:BOOL=NO .endif .if defined(BUILD_PYTHON_MODULE) do-install: ${MKDIR} ${STAGEDIR}${PYTHON_SITELIBDIR} ${INSTALL_DATA} ${INSTALL_WRKSRC}/src/GDL.so ${STAGEDIR}${PYTHON_SITELIBDIR}/ .endif .if !defined(BUILD_PYTHON_MODULE) post-install: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR}/testsuite (cd ${WRKSRC}/testsuite && ${COPYTREE_SHARE} \* ${STAGEDIR}${EXAMPLESDIR}/testsuite/) .endif .if defined(MAINTAINER_MODE) regression-test: install . if defined(BUILD_PYTHON_MODULE) @${ECHO_CMD} 'import GDL' > ${WRKDIR}/testgdl.py @${ECHO_CMD} 'print GDL.function("sin",(1,))' >> ${WRKDIR}/testgdl.py ${PYTHON_CMD} ${WRKDIR}/testgdl.py . else @${ECHO_CMD} ".RUN ${EXAMPLESDIR}/testsuite/test_suite.pro" \ > ${WRKDIR}/testgdl @${ECHO_CMD} "exit" >> ${WRKDIR}/testgdl ${PREFIX}/bin/gdl < ${WRKDIR}/testgdl . endif .endif .include diff --git a/science/hdf/Makefile b/science/hdf/Makefile index a565101a1f89..6dab0d3ef722 100644 --- a/science/hdf/Makefile +++ b/science/hdf/Makefile @@ -1,55 +1,56 @@ # Created by: mi PORTNAME= hdf PORTVERSION= 4.2.15 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= science archivers graphics MASTER_SITES= http://www.hdfgroup.org/ftp/HDF/releases/HDF${PORTVERSION}/src/ \ ftp://ftp.hdfgroup.org/HDF/releases/HDF${PORTVERSION}/src/ MAINTAINER= ports@FreeBSD.org COMMENT= Hierarchical Data Format library (from NCSA) NOT_FOR_ARCHS= aarch64 armv6 armv7 NOT_FOR_ARCHS_REASON= fails to compile: no machine type has been defined -LIB_DEPENDS= libsz.so:science/szip +LIB_DEPENDS= libsz.so:science/libaec CONFLICTS_INSTALL= netcdf-4.[0-9]* USES= fortran jpeg libtool GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-shared --with-jpeg=${LOCALBASE} \ --with-szlib=${LOCALBASE} USE_LDCONFIG= yes INSTALL_TARGET= install-strip TEST_TARGET= check PORTDATA= * PORTEXAMPLES= * OPTIONS_DEFINE= EXAMPLES .include .if ${GCC_DEFAULT} >= 10 # workaround for Type mismatch between actual argument at (1) and actual argument at (2) (CHARACTER(0)/INTEGER(4)). # in theory, this should set FCFLAGS, but the port does not conform FFLAGS+= -fallow-argument-mismatch .endif post-patch: @${REINPLACE_CMD} -e '/PROD_/ s|=.*|=""|' ${WRKSRC}/config/freebsd @${REINPLACE_CMD} -e 's/ || (__APPLE__.*//' \ ${WRKSRC}/hdf/test/fortest.c post-install: ${INSTALL_MAN} ${WRKSRC}/man/hdfunpac.1 \ ${STAGEDIR}${MAN1PREFIX}/man/man1 # Allow to build on PowerPC @${REINPLACE_CMD} -e '/if defined (__APPLE__)/ \ s,),) || defined(__powerpc__),' ${WRKSRC}/hdf/src/hdfi.h ${INSTALL_MAN} ${WRKSRC}/man/gr_chunk.3 \ ${STAGEDIR}${MAN3PREFIX}/man/man3 .include diff --git a/science/hdf5-18/Makefile b/science/hdf5-18/Makefile index a436e9d42621..bb5f149f01ec 100644 --- a/science/hdf5-18/Makefile +++ b/science/hdf5-18/Makefile @@ -1,92 +1,92 @@ # Created by: Wen Heping PORTNAME= hdf5 PORTVERSION= 1.8.21 # When PORTVERSION changes, please update french/med/files/patch-configure -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science archivers graphics MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ \ http://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ \ ftp://ftp.hdfgroup.org/HDF5/releases/hdf5-1.8/${PORTNAME}-${PORTVERSION}/src/ PKGNAMESUFFIX= -18 MAINTAINER= thierry@FreeBSD.org COMMENT= Hierarchical Data Format library (from NCSA) 1.8 LICENSE= BSD4CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING OPTIONS_DEFINE= DEBUG EXAMPLES FORTRAN SZIP USES= cpe libtool:keepla localbase tar:bzip2 CPE_VENDOR= hdfgroup USE_LDCONFIG= yes GNU_CONFIGURE= yes PORTSUFF= ${PORTNAME}${PKGNAMESUFFIX} CONFIGURE_ARGS= --enable-cxx \ --enable-instrument \ --enable-strict-format-checks \ --with-pthread=/usr \ --with-zlib=/usr \ --program-suffix=${PKGNAMESUFFIX} \ --includedir=${PREFIX}/include/${PORTSUFF} EXAMPLESDIR= ${PREFIX}/share/examples/${PORTSUFF} SUFF2FIX= tools/misc/h5cc.in tools/misc/h5redeploy.in \ c++/src/h5c++.in fortran/src/h5fc.in .include .if ${PORT_OPTIONS:MDEBUG} CONFIGURE_ARGS+=--disable-production --enable-debug=all .endif .if ${PORT_OPTIONS:MFORTRAN} USES+= fortran CONFIGURE_ARGS+=--enable-fortran CONFIGURE_ENV+= F9X=${FC} PLIST_SUB+= FORTRAN="" FCFLAGS_f90= ${FCFLAGS} LIBS+= -lstdc++ .else PLIST_SUB+= FORTRAN="@comment " .endif .if ${PORT_OPTIONS:MSZIP} -LIB_DEPENDS+= libsz.so:science/szip +LIB_DEPENDS+= libsz.so:science/libaec CONFIGURE_ARGS+=--with-szlib=${LOCALBASE} .endif pre-configure: ${REINPLACE_CMD} -e 's|-lpthread|${PTHREAD_LIBS}|g' ${WRKSRC}/configure ${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/config/gnu-flags ${REINPLACE_CMD} \ -e '/LD_LIBRARY_PATH/ s|^|#|' \ -e 's|/share/hdf5_examples|/${EXAMPLESDIR_REL}|' \ -e 's|(INSTALL)|(INSTALL_DATA)|' \ `${FIND} ${WRKSRC} -regex '.*/examples/Makefile.in'` ${REINPLACE_CMD} -e 's|\[ -a|\[ -f|g' `${FIND} ${WRKSRC} -name \*.sh\*` .if !${PORT_OPTIONS:MEXAMPLES} ${REINPLACE_CMD} -e '/^install:/ s|install-examples||' ${WRKSRC}/Makefile.in .endif ${FIND} ${WRKSRC} -name Makefile.in | ${XARGS} \ ${REINPLACE_CMD} -e 's|libhdf5|libhdf5${PKGNAMESUFFIX}|g' ${REINPLACE_CMD} -e 's|libhdf5|libhdf5${PKGNAMESUFFIX}|g' \ ${WRKSRC}/test/testlibinfo.sh.in .for pf in ${SUFF2FIX} ${REINPLACE_CMD} -e 's|%%SUFF%%|${PKGNAMESUFFIX}|g' ${WRKSRC}/${pf} .endfor post-configure: ${CP} -p ${WRKSRC}/src/libhdf5.settings.in \ ${WRKSRC}/src/libhdf5${PKGNAMESUFFIX}.settings.in ${CP} -p ${WRKSRC}/src/libhdf5.settings \ ${WRKSRC}/src/libhdf5${PKGNAMESUFFIX}.settings post-stage: .if ${PORT_OPTIONS:MFORTRAN} ${MV} ${STAGEDIR}${PREFIX}/bin/h5fc ${STAGEDIR}${PREFIX}/bin/h5fc${PKGNAMESUFFIX} .endif regression-test test: build cd ${WRKSRC}/ && ${SETENV} ${MAKE_ENV} ${MAKE} check .include diff --git a/science/hdf5/Makefile b/science/hdf5/Makefile index 5b5039aed81a..8e0133176a16 100644 --- a/science/hdf5/Makefile +++ b/science/hdf5/Makefile @@ -1,59 +1,60 @@ # Created by: ijliao PORTNAME= hdf5 PORTVERSION= 1.10.6 +PORTREVISION= 1 PORTEPOCH= 1 CATEGORIES= science archivers graphics MASTER_SITES= https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${PORTVERSION:R}/${DISTNAME}/src/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= Hierarchical Data Format library (from NCSA) LICENSE= BSD4CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING CONFLICTS_INSTALL= hdf-4.[0-9]* hdf5-1.6.[0-9]* OPTIONS_DEFINE= DEBUG EXAMPLES FORTRAN SZIP OPTIONS_RADIO= SUPPORT OPTIONS_RADIO_SUPPORT= CXX PARALLEL OPTIONS_DEFAULT=CXX SZIP OPTIONS_SUB= yes PARALLEL_DESC= Parallel support USES= compiler:c11 cpe libtool localbase tar:bzip2 CPE_VENDOR= hdfgroup CONFIGURE_ARGS= --enable-hl \ --enable-instrument \ --enable-strict-format-checks GNU_CONFIGURE= yes INSTALL_TARGET= install-strip MAKE_JOBS_UNSAFE= yes TEST_TARGET= check USE_LDCONFIG= yes PORTEXAMPLES= * CXX_CONFIGURE_ENABLE= cxx DEBUG_CONFIGURE_OFF= --enable-build-mode=production DEBUG_CONFIGURE_ON= --enable-build-mode=debug FORTRAN_CONFIGURE_ENABLE= fortran FORTRAN_CONFIGURE_ENV= F9X=${FC} FORTRAN_USES= fortran PARALLEL_CONFIGURE_ENABLE= parallel PARALLEL_LDFLAGS= -L${LOCALBASE}/lib -lmpi PARALLEL_LIB_DEPENDS= libmpi.so:net/mpich SZIP_CONFIGURE_ON= --with-szlib=${LOCALBASE} -SZIP_LIB_DEPENDS= libsz.so:science/szip +SZIP_LIB_DEPENDS= libsz.so:science/libaec post-patch: @${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/config/gnu-flags @${REINPLACE_CMD} \ -e '/LD_LIBRARY_PATH/ s|^|#|' \ -e 's|/share/hdf5_examples|/${EXAMPLESDIR_REL}|' \ -e 's|(INSTALL)|(INSTALL_DATA)|' \ `${FIND} ${WRKSRC} -regex '.*/examples/Makefile.in'` @${REINPLACE_CMD} -e 's|\[ -a|\[ -f|g' `${FIND} ${WRKSRC} -name \*.sh\*` .include diff --git a/science/helfem/Makefile b/science/helfem/Makefile index 1ef0c371f7c4..af210d8e0afd 100644 --- a/science/helfem/Makefile +++ b/science/helfem/Makefile @@ -1,27 +1,27 @@ PORTNAME= helfem DISTVERSION= g20210912 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Finite element methods for electronic structure calculations LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libarmadillo.so:math/armadillo \ libgsl.so:math/gsl \ libhdf5_cpp.so:science/hdf5 \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libxc.so:science/libxc USES= cmake fortran USE_GITHUB= yes GH_ACCOUNT= susilehtola GH_PROJECT= HelFEM GH_TAGNAME= 21461e9 CMAKE_ON= HELFEM_FIND_DEPS BUILD_SHARED_LIBS .include diff --git a/science/lammps/Makefile b/science/lammps/Makefile index f0915f1d1df9..a6d9c6d3a0e0 100644 --- a/science/lammps/Makefile +++ b/science/lammps/Makefile @@ -1,151 +1,152 @@ PORTNAME= lammps PORTVERSION= ${GH_TAGNAME:C/(stable|patch)_([0-9]{1,2})([A-Z][a-z][a-z])([0-9]{4})/\4.\3.\2/S/Jan/01/S/Feb/02/S/Mar/03/S/Apr/04/S/May/05/S/Jun/06/S/Jul/07/S/Aug/08/S/Sep/09/S/Oct/10/S/Nov/11/S/Dec/12/} +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Classical molecular dynamics code with a focus on materials modeling LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= undefined reference to `__atomic_load' CONFLICTS_BUILD= ga mpich mpich2 # conflicts with include/error.h from ga, already fixed in the head LIB_DEPENDS= libevent.so:devel/libevent \ libfftw3.so:math/fftw3 \ libhwloc.so:devel/hwloc2 \ libnghttp2.so:www/libnghttp2 \ libpciaccess.so:devel/libpciaccess \ libssh2.so:security/libssh2 \ libzstd.so:archivers/zstd USES= blaslapack:openblas cmake:noninja compiler:c++14-lang eigen:3 fortran gnome localbase:ldflags python shebangfix USE_GNOME= libxml2 USE_LDCONFIG= yes USE_PYTHON= cython USE_GITHUB= yes GH_TAGNAME= patch_2Jun2022 SHEBANG_GLOB= *.sh *.bash SHEBANG_FILES= lib/kokkos/bin/nvcc_wrapper CMAKE_ON= BUILD_SHARED_LIBS CMAKE_SOURCE_PATH= ${WRKSRC}/cmake CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" ${CMAKE_ARGS_${CHOSEN_COMPILER_TYPE}} \ -DPython_EXECUTABLE=${PYTHON_CMD} CMAKE_ARGS_gcc= -DBUILD_OMP:BOOL=false # enable packages (for a complete list see STANDARD_PACKAGES in cmake/CMakeLists.txt) CMAKE_ON+= PKG_ASPHERE PKG_ATC PKG_AWPMD PKG_BOCS PKG_BODY PKG_BROWNIAN PKG_CG-DNA PKG_CG-SDK PKG_CLASS2 CMAKE_ON+= PKG_COLLOID PKG_COLVARS PKG_COMPRESS PKG_DIELECTRIC PKG_DIFFRACTION PKG_DIPOLE PKG_DPD-BASIC PKG_DPD-MESO PKG_DPD-REACT PKG_DPD-SMOOTH CMAKE_ON+= PKG_DRUDE PKG_EFF PKG_EXTRA-COMPUTE PKG_EXTRA-DUMP PKG_EXTRA-FIX PKG_EXTRA-MOLECULE PKG_EXTRA-PAIR PKG_FEP PKG_GRANULAR PKG_H5MD CMAKE_ON+= PKG_INTERLAYER PKG_KIM PKG_KSPACE PKG_LATBOLTZ PKG_LATTE PKG_MACHDYN PKG_MANIFOLD PKG_MANYBODY PKG_MC CMAKE_ON+= PKG_MEAM PKG_MESSAGE PKG_MGPT PKG_MISC PKG_ML-IAP PKG_ML-RANN CMAKE_ON+= PKG_ML-SNAP PKG_MOFFF PKG_MOLECULE PKG_MOLFILE PKG_MPIIO PKG_ORIENT PKG_PERI PKG_PHONON CMAKE_ON+= PKG_PLUGIN PKG_PLUMED PKG_POEMS PKG_PTM PKG_PYTHON PKG_QEQ PKG_QMMM PKG_QTB PKG_REACTION PKG_REAXFF CMAKE_ON+= PKG_REPLICA PKG_RIGID PKG_SHOCK PKG_SMTBQ PKG_SPH PKG_SPIN PKG_SRD PKG_TALLY PKG_UEF CMAKE_ON+= PKG_VORONOI PKG_YAFF # Packages requiring extra downloades or dependencies: PKG_MSCG PKG_ADIOS PKG_MDI PKG_MESONT PKG_ML-PACE PKG_NETCDF PKG_ML-QUIP PKG_SCAFACOS PKG_VTK # PKG_ML-HDNNP downloads https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz OPTIONS_DEFINE= EXCEPTIONS JPEG PNG GZIP FFMPEG OPTIONS_GROUP= PARALLEL PACKAGES OPTIONS_DEFAULT= EXCEPTIONS MPI OPENMP JPEG PNG GZIP FFMPEG H5MD KIM KOKKOS LATTE PLUMED VORONOI ${OPTIONS_DEFAULT_${CHOSEN_COMPILER_TYPE}} OPTIONS_SUB= yes PARALLEL_DESC= Enable parallelizations: PACKAGES_DESC= Enable packages: OPTIONS_GROUP_PARALLEL= MPI OPENMP ${OPTIONS_DEFINE_${CHOSEN_COMPILER_TYPE}} OPTIONS_GROUP_PACKAGES= H5MD KIM KOKKOS LATTE PLUMED VORONOI VTK EXCEPTIONS_DESC= Enable the use of C++ exceptions EXCEPTIONS_CMAKE_BOOL= LAMMPS_EXCEPTIONS MPI_CMAKE_BOOL= BUILD_MPI PKG_MPIIO PKG_USER-LB MPI_LIB_DEPENDS= libmpi.so:net/openmpi MPI_USES= compiler:c11 FFMPEG_CMAKE_BOOL= WITH_FFMPEG FFMPEG_BUILD_DEPENDS= ffmpeg:multimedia/ffmpeg FFMPEG_RUN_DEPENDS= ffmpeg:multimedia/ffmpeg JPEG_CMAKE_BOOL= WITH_JPEG JPEG_USES= jpeg PNG_CMAKE_BOOL= WITH_PNG PNG_LIB_DEPENDS= libpng.so:graphics/png GZIP_DESC= Enable GZIP support GZIP_CMAKE_BOOL= WITH_GZIP H5MD_DESC= USER-H5MD package based on libhdf5 H5MD_CMAKE_BOOL= PKG_USER-H5MD H5MD_LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec KIM_DESC= KIM package based on the OpenKim library/repository KIM_USES= pkgconfig KIM_CMAKE_BOOL= PKG_KIM KIM_CMAKE_ON= -DDOWNLOAD_KIM:BOOL=OFF KIM_LIB_DEPENDS= libkim-api.so:science/kim-api \ libcurl.so:ftp/curl KIM_RUN_DEPENDS= openkim-models>0:science/openkim-models KOKKOS_DESC= kokkos package based on the libkokkos library KOKKOS_CMAKE_BOOL= PKG_KOKKOS EXTERNAL_KOKKOS KOKKOS_LIB_DEPENDS= libkokkoscore.so:devel/kokkos LATTE_DESC= latte package based on the liblatte library LATTE_CMAKE_BOOL= PKG_LATTE LATTE_LIB_DEPENDS= liblatte.so:science/latte PLUMED_DESC= plumed package based on the plumed library PLUMED_USES= pkgconfig PLUMED_CMAKE_BOOL= PKG_USER-PLUMED PLUMED_CMAKE_ON= -DPLUMED_MODE=shared PLUMED_LIB_DEPENDS= libplumed.so:science/plumed VORONOI_DESC= voro++, Voronoi tessellation package VORONOI_CMAKE_BOOL= PKG_VORONOI VORONOI_LIB_DEPENDS= libvoro++.so:science/voro++ VTK_DESC= USER-VTK package based on the external vtk package VTK_CMAKE_BOOL= PKG_USER-VTK VTK_CMAKE_ON= -DVTK_DIR:PATH=${LOCALBASE}/lib/vtk-8.2/cmake/vtk-8.2 VTK_USES= qt:5 xorg VTK_USE= qt=core,gui,sql,widgets xorg=ice,sm,x11,xext,xt VTK_LIB_DEPENDS= libvtkImagingMath-8.2.so:math/vtk8 \ libexpat.so:textproc/expat2 \ libfreetype.so:print/freetype2 \ libtiff.so:graphics/tiff PORTSCOUT= ignore:1 # due to a special version tagging scheme that this project uses portscout fails to find new versions, watching their GitHub release page instead .include .if ${PORT_OPTIONS:MOPENMP} CMAKE_ARGS+= -DBUILD_OMP:BOOL=true .endif xpost-patch: # adjust SHELL in Makefile @${REINPLACE_CMD} 's|SHELL = /bin/bash|SHELL = ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/Makefile # fix python version, also see https://github.com/lammps/lammps/issues/3098, https://github.com/lammps/lammps/issues/3099 @${FIND} ${WRKSRC} -name "CMakeLists.txt" -o -name "*.cmake" | ${XARGS} ${REINPLACE_CMD} -e ' \ s|find_package(Python3 REQUIRED |find_package(Python $${FREEBSD_PYTHON_VER} EXACT REQUIRED |; \ s|find_package(Python 3.5 COMPONENTS |find_package(Python $${FREEBSD_PYTHON_VER} EXACT COMPONENTS |; \ s|find_package(Python 3.6 COMPONENTS |find_package(Python $${FREEBSD_PYTHON_VER} EXACT COMPONENTS |; \ s|find_package(Python3 REQUIRED |find_package(Python $${FREEBSD_PYTHON_VER} EXACT REQUIRED |; \ s|find_package(Python COMPONENTS |find_package(Python3 $${FREEBSD_PYTHON_VER} EXACT COMPONENTS |; \ s|find_package(Python3 COMPONENTS |find_package(Python3 $${FREEBSD_PYTHON_VER} EXACT COMPONENTS |; \ s|find_package(Python QUIET COMPONENTS |find_package(Python3 $${FREEBSD_PYTHON_VER} EXACT QUIET COMPONENTS |; \ s|find_package(Python REQUIRED COMPONENTS |find_package(Python3 $${FREEBSD_PYTHON_VER} EXACT REQUIRED COMPONENTS | \ ' post-patch-FFMPEG-off: @${REINPLACE_CMD} 's|find_program(FFMPEG_EXECUTABLE|#&|' ${WRKSRC}/cmake/CMakeLists.txt post-install: @${RM} -r ${STAGEDIR}${PREFIX}/lib/python* .include diff --git a/science/netcdf/Makefile b/science/netcdf/Makefile index 01df33791388..c749369cfa21 100644 --- a/science/netcdf/Makefile +++ b/science/netcdf/Makefile @@ -1,54 +1,55 @@ # Created by: Sunpoet Po-Chuan Hsieh PORTNAME= netcdf PORTVERSION= 4.8.1 +PORTREVISION= 1 DISTVERSIONPREFIX= c- CATEGORIES= science MASTER_SITES= https://downloads.unidata.ucar.edu/netcdf-c/${PORTVERSION}/ \ LOCAL/sunpoet MAINTAINER= sunpoet@FreeBSD.org COMMENT= C library for machine-independent, array-oriented data access LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYRIGHT LIB_DEPENDS= libcurl.so:ftp/curl \ libhdf5.so:science/hdf5 USES= gmake libtool localbase ncurses pathfix pkgconfig:run CONFIGURE_ARGS= --disable-filter-testing \ --enable-byterange --enable-dap --enable-netcdf-4 CPPFLAGS+= -fPIC -DPIC GNU_CONFIGURE= yes INSTALL_TARGET= install-strip LIBS+= -lexecinfo TEST_TARGET= check USE_LDCONFIG= yes CONFLICTS_INSTALL= hdf-4.[0-9]* netcdf-3.[0-9]* netcdf3-3.[0-9]* OPTIONS_DEFINE= DOCS DOXYGEN SZIP OPTIONS_DEFAULT=SZIP OPTIONS_SUB= yes DOXYGEN_IMPLIES=DOCS SZIP_DESC= SZIP support (required if HDF5 was built with SZIP) DOXYGEN_BUILD_DEPENDS= doxygen:devel/doxygen DOXYGEN_CONFIGURE_ENABLE= doxygen -SZIP_LIB_DEPENDS= libsz.so:science/szip +SZIP_LIB_DEPENDS= libsz.so:science/libaec SZIP_LIBS= -lsz post-patch: @${REINPLACE_CMD} -e 's|-ldl ||g' ${WRKSRC}/configure @${REINPLACE_CMD} -e '/ int fileno(FILE\*);/d' ${WRKSRC}/libdispatch/d*.c ${WRKSRC}/ncgen/ncgen* ${WRKSRC}/ncgen3/ncgen* ${WRKSRC}/oc2/ocdump.c post-build-DOXYGEN-on: cd ${WRKSRC}/docs/ && ${LOCALBASE}/bin/doxygen . post-install-DOXYGEN-on: ${MKDIR} ${STAGEDIR}${DOCSDIR}/ cd ${WRKSRC}/docs/html/ && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} .include diff --git a/science/openems/Makefile b/science/openems/Makefile index 3296973eba6c..26bd10ad482e 100644 --- a/science/openems/Makefile +++ b/science/openems/Makefile @@ -1,45 +1,45 @@ PORTNAME= openems DISTVERSIONPREFIX= v DISTVERSION= 0.0.35-71 DISTVERSIONSUFFIX= -g4c24b6e -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Electromagnetic field solver using the EC-FDTD method LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING ONLY_FOR_ARCHS= amd64 powerpc64 powerpc64le ONLY_FOR_ARCHS_REASON= upstream only supports amd64 and powerpc64 # many dependencies below are induced by vtk8, but not vtk9 LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libCSXCAD.so:cad/csxcad \ libexpat.so:textproc/expat2 \ libfparser-4.5.so:math/fparser \ libhdf5.so:science/hdf5 \ libpng16.so:graphics/png \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libtiff.so:graphics/tiff \ libtinyxml.so:textproc/tinyxml \ libvtkCommonCore-8.2.so:math/vtk8 # some related packages don't support vtk9 yet, see https://github.com/thliebig/QCSXCAD/issues/6#issuecomment-901633240 USES= cmake jpeg pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= thliebig GH_PROJECT= openEMS CMAKE_ARGS= -DVTK_DIR=${LOCALBASE}/lib/vtk-8.2/cmake/vtk-8.2 CXXFLAGS+= -I${LOCALBASE}/include/fparser # fparser.pc probably returns a wrong value DATADIR= ${PREFIX}/share/openEMS post-install: @${REINPLACE_CMD} -i '' -e 's|#!/bin/bash|#!/bin/sh|' ${STAGEDIR}${PREFIX}/bin/openEMS.sh .include diff --git a/science/openmc/Makefile b/science/openmc/Makefile index 2379ec674c0b..8484d49c19d7 100644 --- a/science/openmc/Makefile +++ b/science/openmc/Makefile @@ -1,43 +1,44 @@ PORTNAME= openmc DISTVERSIONPREFIX= v DISTVERSION= 0.13.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Monte Carlo neutron and photon transport simulation code LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= xtensor>0:math/xtensor LIB_DEPENDS= libfmt.so:devel/libfmt \ libhdf5.so:science/hdf5 \ libpng16.so:graphics/png \ libpugixml.so:textproc/pugixml \ - libsz.so:science/szip + libsz.so:science/libaec USES= cmake:noninja eigen:3 pkgconfig USE_GITHUB= yes GH_ACCOUNT= ${PORTNAME}-dev GH_TUPLE= martinmoene:gsl-lite:913e86d:gsl_lite/vendor/gsl-lite BINARY_ALIAS= git=false OPTIONS_DEFINE= LIBMESH MPI OPENMP OPTIONS_DEFAULT= MPI OPENMP LIBMESH_DESC= Support for libMesh unstructured mesh tallies LIBMESH_CMAKE_BOOL= libmesh LIBMESH_LIB_DEPENDS= libmesh_opt.so:math/libmesh MPI_VARS= CXX=${LOCALBASE}/bin/mpic++ # compilation breaks with OpenMPI-{3,4} and LIBMESH=ON MPI_BUILD_DEPENDS= mpich>0:net/mpich MPI_RUN_DEPENDS= mpich>0:net/mpich OPENMP_CMAKE_BOOL= openmp post-install: ${RM} -r ${STAGEDIR}${DOCSDIR} .include diff --git a/science/openmolcas/Makefile b/science/openmolcas/Makefile index 036beeae13b3..bd4fb73e8cd4 100644 --- a/science/openmolcas/Makefile +++ b/science/openmolcas/Makefile @@ -1,50 +1,51 @@ PORTNAME= openmolcas DISTVERSION= 22.02 +PORTREVISION= 1 CATEGORIES= science # chemistry MAINTAINER= yuri@FreeBSD.org COMMENT= Quantum chemistry software package LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= build breaks: Symbol 'maxfilesize' at (1) has no IMPLICIT type; did you mean 'mxfile'? BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pyparsing>0:devel/py-pyparsing@${PY_FLAVOR} LIB_DEPENDS= libhdf5.so:science/hdf5 \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libxc.so:science/libxc USES= cmake fortran python shebangfix USE_GCC= yes # see https://gitlab.com/Molcas/OpenMolcas/-/issues/351 USE_GITLAB= yes GL_ACCOUNT= Molcas GL_PROJECT= OpenMolcas GL_COMMIT= f8df69cf87b241a15ebc82d72a8f9a031a385dd4 USE_GITHUB= nodefault GH_TUPLE= Reference-LAPACK:lapack:aa631b4b:lapack/External/lapack \ libwfa:libwfa:bbe3392a:libwfa/External/libwfa SHEBANG_FILES= sbin/help_doc sbin/help_func sbin/help_basis sbin/setup sbin/verify sbin/version CMAKE_ARGS= -DEXTERNAL_LIBXC:STRING=${LOCALBASE} \ -DFREEBSD_PYTHON_VER:STRING=${PYTHON_VER} #CMAKE_ON= # for EFPLIB, MSYM see https://gitlab.com/Molcas/OpenMolcas/-/issues/350, for WFA - hdf5 needs updating CMAKE_OFF= BUILD_TESTING CMAKE_INSTALL_PREFIX= ${DATADIR} # installed into DATADIR because it doesn't respect UNIX file path conventions, see https://gitlab.com/Molcas/OpenMolcas/-/issues/352 BINARY_ALIAS= cpp=${CPP} # cpp is called from cmake scripts post-install: # remove unused static libraries, see https://gitlab.com/Molcas/OpenMolcas/-/issues/354 @${RM} -r ${STAGEDIR}${CMAKE_INSTALL_PREFIX}/lib # remove unnecessary fines @${RM} ${STAGEDIR}${CMAKE_INSTALL_PREFIX}/CONTRIBUTORS.md @${RM} ${STAGEDIR}${CMAKE_INSTALL_PREFIX}/LICENSE # remove empty doc directory @${RMDIR} ${STAGEDIR}${DATADIR}/doc .include diff --git a/science/py-PyNE/Makefile b/science/py-PyNE/Makefile index d8576edc4521..5cbc40b3dce0 100644 --- a/science/py-PyNE/Makefile +++ b/science/py-PyNE/Makefile @@ -1,75 +1,75 @@ PORTNAME= PyNE DISTVERSION= 0.7.7 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science MASTER_SITES= http://raw.githubusercontent.com/pyne/data/master/:decay \ http://raw.githubusercontent.com/pyne/data/master/:cram \ http://raw.githubusercontent.com/pyne/data/master/:dlc \ http://raw.githubusercontent.com/pyne/data/master/:clc \ https://github.com/pyne/data/raw/master/:nuc_data PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTFILES= decay.tar.gz:decay \ cram.tar.gz:cram \ decay-linux-clang.tar.gz:dlc \ cram-linux-clang.tar.gz:clc \ prebuilt_nuc_data.h5:nuc_data DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} EXTRACT_ONLY= ${DISTNAME}.tar.gz MAINTAINER= yuri@FreeBSD.org COMMENT= PyNE: The Nuclear Engineering Toolkit LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}tables>0:devel/py-tables@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} BUILD_DEPENDS= cmake:devel/cmake \ ${PY_DEPENDS} LIB_DEPENDS= libhdf5.so:science/hdf5 \ libMOAB.so:math/moab \ - libsz.so:science/szip + libsz.so:science/libaec RUN_DEPENDS= ${PY_DEPENDS} USES= compiler:c++17-lang fortran python:3.7+ USE_PYTHON= distutils cython flavors USE_GITHUB= yes GH_ACCOUNT= pyne GH_PROJECT= pyne MAKE_ENV= DESTDIR=${STAGEDIR} FFLAGS+= -fallow-argument-mismatch # all arguments are described here: http://pyne.io/install/source.html#source PY_EXTRA_ARGS= --slow # this chooses slow compilation of sources from {decay,cram}.tar.gz # over incompatible pre-compiled assembly from {decay,cram}-linux-clang.tar.gz PY_EXTRA_ARGS+= ${_MAKE_JOBS} PY_EXTRA_ARGS+= --hdf5 ${LOCALBASE} PY_EXTRA_ARGS+= --moab ${LOCALBASE} PYDISTUTILS_CONFIGUREARGS= ${PY_EXTRA_ARGS} PYDISTUTILS_BUILDARGS= ${PY_EXTRA_ARGS} BINARY_ALIAS= python=${PYTHON_CMD} post-extract: .for f in decay.tar.gz cram.tar.gz decay-linux-clang.tar.gz cram-linux-clang.tar.gz @${CP} ${DISTDIR}/${DIST_SUBDIR}/${f} ${WRKSRC}/src .endfor do-install: # install project cd ${INSTALL_WRKSRC} && \ ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYDISTUTILS_SETUP} ${PYDISTUTILS_INSTALL_TARGET} # also install nuc_data.h5 because it is referred to in the code and is required by Jupyter notebooks ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/prebuilt_nuc_data.h5 ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/nuc_data.h5 # strip ${STRIP_CMD} \ ${STAGEDIR}${LOCALBASE}/lib/lib*.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/*.so \ ${STAGEDIR}${PYTHON_SITELIBDIR}/pyne/xs/models.so .include diff --git a/science/qmcpack/Makefile b/science/qmcpack/Makefile index cc276157ea05..6585d76306a8 100644 --- a/science/qmcpack/Makefile +++ b/science/qmcpack/Makefile @@ -1,63 +1,63 @@ PORTNAME= qmcpack DISTVERSIONPREFIX= v DISTVERSION= 3.14.0 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Many-body ab initio Quantum Monte Carlo code for quantum chemistry LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= undefined reference to `__atomic_load' LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libfftw3.so:math/fftw3 \ libhdf5.so:science/hdf5 \ libmpich.so:net/mpich \ libopenblas.so:math/openblas \ - libsz.so:science/szip + libsz.so:science/libaec TEST_DEPENDS= bash:shells/bash USES= cmake:testing compiler:c++17-lang fortran gnome localbase:ldflags pkgconfig python shebangfix USE_GNOME= libxml2 USE_GITHUB= yes GH_ACCOUNT= ${PORTNAME:tu} SHEBANG_FILES= src/QMCTools/gpaw4qmcpack.py \ ${NEXUS_PLIST_FILES:C/^/nexus\//} SHEBANG_GLOB= check.sh CMAKE_OFF= BUILD_UNIT_TESTS CMAKE_ARGS= -DFREEBSD_PYTHON_VER=${PYTHON_VER} CMAKE_TESTING_ON= BUILD_UNIT_TESTS # at least 3 testcases are known to fail PROGS= convert4qmc convertpw4qmc gpaw4qmcpack.py ppconvert qmc-check-affinity qmc-extract-eshdf-kvectors qmc-get-supercell qmcfinitesize qmcpack qmcpack.settings PLIST_FILES= ${PROGS:C/^/bin\//} BINARY_ALIAS= python=${PYTHON_CMD} python3=${PYTHON_CMD} OPTIONS_DEFINE= NEXUS OPTIONS_DEFAULT= NEXUS OPTIONS_SUB= yes NEXUS_DESC= Install Nexus (workflow utility) alongside QMCPACK NEXUS_CMAKE_BOOL= INSTALL_NEXUS NEXUS_PY_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyscf>0:science/py-pyscf@${PY_FLAVOR} NEXUS_BUILD_DEPENDS= ${NEXUS_PY_DEPENDS} NEXUS_RUN_DEPENDS= ${NEXUS_PY_DEPENDS} NEXUS_PLIST_FILES= bin/eshdf \ bin/nxs-redo \ bin/nxs-sim \ bin/nxs-test \ bin/qdens \ bin/qdens-radial \ bin/qmc-fit \ bin/qmca .include diff --git a/science/rmf/Makefile b/science/rmf/Makefile index 5a463b58eefd..8500a6338333 100644 --- a/science/rmf/Makefile +++ b/science/rmf/Makefile @@ -1,33 +1,33 @@ PORTNAME= rmf DISTVERSION= 1.4 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science graphics MAINTAINER= yuri@FreeBSD.org COMMENT= Library to support reading and writing of Rich Molecular Format files LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libboost_system.so:devel/boost-libs \ libhdf5.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec USES= compiler:c++17-lang cmake python:build shebangfix USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= salilab SHEBANG_GLOB= *.py BINARY_ALIAS= python=${PYTHON_CMD} do-test: @${RM} ${WRKSRC}/test/*.py @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DFREEBSD_BUILS_WITH_TESTS:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include diff --git a/science/votca/Makefile b/science/votca/Makefile index 047a995587a3..0a05b64299e6 100644 --- a/science/votca/Makefile +++ b/science/votca/Makefile @@ -1,65 +1,65 @@ PORTNAME= votca DISTVERSIONPREFIX= v DISTVERSION= 2022 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science PATCH_SITES= https://github.com/${GH_ACCOUNT}/${PORTNAME}/commit/ PATCHFILES= 078c6814797749cd1b92a2b19f0302265ccf6463.patch:-p1 # fix testsuite build MAINTAINER= yuri@FreeBSD.org COMMENT= CSG and XTP: libraries for atomistic simulations LICENSE= APACHE20 BROKEN_i386= undefined reference to `__atomic_load' PY_DEPENDS= ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ rdkit>0:science/rdkit BUILD_DEPENDS= bash:shells/bash \ lmp:science/lammps \ ${PY_DEPENDS} LIB_DEPENDS= libboost_program_options.so:devel/boost-libs \ libecpint.so:science/libecpint \ libexpat.so:textproc/expat2 \ libfftw3.so:math/fftw3 \ libgromacs_d.so:science/gromacs \ libhdf5.so:science/hdf5 \ libint2.so:science/libint2 \ - libsz.so:science/szip \ + libsz.so:science/libaec \ libxc.so:science/libxc RUN_DEPENDS= bash:shells/bash \ ${PYNUMPY} \ ${PY_DEPENDS} TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>0:devel/py-pytest@${PY_FLAVOR} USES= cmake compiler:c++14-lang eigen:3 perl5 pkgconfig python:run \ shebangfix USE_GITHUB= yes USE_LDCONFIG= yes SHEBANG_GLOB= *.sh *.pl *.py SHEBANG_FILES= csg/scripts/csg_call.in csg/scripts/csg_inverse.in \ tools/scripts/votca_compare.in tools/scripts/votca_help2doc.in \ xtp/scripts/xtp_update_mapfile.in xtp/scripts/xtp_basisset.in xtp/share/benchmark/xtp_benchmark.in xtp/scripts/xtp_autogen_mapping.in \ xtp/scripts/xtp_modify_jobfile.in \ xtp/scripts/xtp_qmmm2qm.in CMAKE_ON= BUILD_XTP CMAKE_ARGS= -DPython_EXECUTABLE=${PYTHON_CMD} OPTIONS_DEFINE= APPS OPTIONS_DEFAULT= APPS OPTIONS_SUB= yes APPS_DESC= Build applications APPS_CMAKE_BOOL= BUILD_CSGAPPS do-test: @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DENABLE_TESTING:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include diff --git a/sysutils/slurm-wlm/Makefile b/sysutils/slurm-wlm/Makefile index f3dd6e9c9b11..f45ae5d8ddca 100644 --- a/sysutils/slurm-wlm/Makefile +++ b/sysutils/slurm-wlm/Makefile @@ -1,135 +1,136 @@ PORTNAME= slurm DISTVERSION= 20.02.7 +PORTREVISION= 1 CATEGORIES= sysutils python MASTER_SITES= https://download.schedmd.com/slurm/ PKGNAMESUFFIX= -wlm MAINTAINER= ports@FreeBSD.org COMMENT= Simple Linux Utility for Resource Management LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/COPYING NOT_FOR_ARCHS= armv6 armv7 i386 mips powerpc powerpcspe NOT_FOR_ARCHS_REASON= 32-bit support is deprecated LIB_DEPENDS= libjson-c.so:devel/json-c \ libsysinfo.so:devel/libsysinfo \ libmunge.so:security/munge \ liblz4.so:archivers/liblz4 USES= compiler:c11 cpe gmake gnome libtool localbase lua pkgconfig \ python:build readline shebangfix ssl tar:bz2 CPE_VENDOR= schedmd USE_LDCONFIG= yes USE_RC_SUBR= slurmctld slurmd USERS= slurm GROUPS= ${USERS} GNU_CONFIGURE= yes INSTALL_TARGET= install-strip PLIST_SUB= PORTVERSION="${PORTVERSION}" SHEBANG_FILES= doc/html/shtml2html.py doc/man/man2html.py OPTIONS_DEFINE= CURL DOCS GUI HDF5 HWLOC IPMI MYSQL RRD OPTIONS_DEFAULT= HDF5 HWLOC OPTIONS_SUB= yes CURL_DESC= Require cURL for elasticsearch plugins GUI_DESC= Build sview GUI config tool HDF5_DESC= Job profiling using HDF5 HWLOC_DESC= Portable hardware locality IPMI_DESC= IPMI energy consumption accounting RRD_DESC= RRD external sensor data collection DOCS_BUILD_DEPENDS= man2html:textproc/man2html CURL_LIB_DEPENDS= libcurl.so:ftp/curl CURL_CONFIGURE_WITH= libcurl GUI_USE= GNOME=cairo,gdkpixbuf2,glib20,gtk20 GUI_LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 GUI_USES= gettext GUI_CONFIGURE_ENABLE= glibtest gtktest x11 # Neither of these work. See post-patch below. #GTK2_CONFIGURE_ENV_OFF= ac_gtk_test=no #GTK2_CONFIGURE_OFF= --disable-gtktest HDF5_LIB_DEPENDS= libhdf5_cpp.so:science/hdf5 \ - libsz.so:science/szip + libsz.so:science/libaec HDF5_CONFIGURE_WITH= hdf5 HDF5_CONFIGURE_ENV= H5CC=${LOCALBASE}/bin/h5cc HWLOC_LIB_DEPENDS= libhwloc.so.15:devel/hwloc2 HWLOC_CONFIGURE_WITH= hwloc IPMI_LIB_DEPENDS= libfreeipmi.so:sysutils/freeipmi IPMI_CONFIGURE_WITH= freeipmi MYSQL_USES= mysql MYSQL_CONFIGURE_OFF= --with-mysql_config=/nonexistent RRD_LIB_DEPENDS= librrd.so:databases/rrdtool RRD_CONFIGURE_WITH= rrdtool # --docdir is non-functional # CONFIGURE_ARGS= --docdir=${DOCSDIR} # FreeBSD Infiniband support is still experimental # slurmrestd does not build on FreeBSD CONFIGURE_ARGS= --without-ofed --disable-slurmrestd DOCSDIR= ${PREFIX}/share/doc/${PORTNAME}-${DISTVERSION} CFLAGS+= -I${WRKSRC}/slurm -I${LOCALBASE}/include -fcommon LDFLAGS+= -L${LOCALBASE}/lib -lsysinfo -lprocstat -fcommon # Hack around nonfunctional --disable-gtktest flag pre-configure-GUI-off: @${REINPLACE_CMD} -e 's|min_gtk_version=.*|min_gtk_version=2000.0.0|' \ ${WRKSRC}/configure # SLURM's configure enables interactive jobs if pty.h exists. Replacing # #include with appropriate headers will therefore not work, so instead # add a pty.h for the build. pre-configure: @${CP} ${FILESDIR}/pty.h ${WRKSRC}/slurm @${REINPLACE_CMD} -e 's|sched_setaffinity|cpuset_setaffinity|g' \ -e 's|%%LOCALBASE%%|${LOCALBASE}|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|"/proc|"/compat/linux/proc|g' \ -e 's|(/proc)|(/compat/linux/proc)|g' \ ${WRKSRC}/src/slurmd/slurmstepd/req.c \ ${WRKSRC}/src/slurmd/slurmstepd/pdebug.c \ ${WRKSRC}/src/slurmd/common/xcpuinfo.c \ ${WRKSRC}/src/slurmd/common/xcgroup.c \ ${WRKSRC}/src/slurmd/common/set_oomadj.c \ ${WRKSRC}/src/slurmd/common/proctrack.c \ ${WRKSRC}/src/common/callerid.c \ ${WRKSRC}/src/plugins/task/affinity/affinity.c \ ${WRKSRC}/src/plugins/acct_gather_energy/rapl/acct_gather_energy_rapl.c \ ${WRKSRC}/src/plugins/jobacct_gather/cgroup/jobacct_gather_cgroup.c \ ${WRKSRC}/src/plugins/jobacct_gather/common/common_jag.c \ ${WRKSRC}/src/plugins/jobacct_gather/linux/jobacct_gather_linux.c \ ${WRKSRC}/src/plugins/switch/cray_aries/scaling.c \ ${WRKSRC}/src/plugins/proctrack/cray_aries/proctrack_cray_aries.c \ ${WRKSRC}/src/plugins/proctrack/cgroup/proctrack_cgroup.c \ ${WRKSRC}/src/plugins/proctrack/pgid/proctrack_pgid.c \ ${WRKSRC}/src/plugins/proctrack/linuxproc/kill_tree.c \ ${WRKSRC}/src/plugins/acct_gather_filesystem/lustre/acct_gather_filesystem_lustre.c \ ${WRKSRC}/src/plugins/node_features/knl_generic/node_features_knl_generic.c \ ${WRKSRC}/contribs/cray/pam_job.c @if ${WHICH} sbatch > /dev/null; then \ ${ECHO_CMD} "********************************************"; \ ${ECHO_CMD} "Build may fail while slurm-wlm is installed."; \ ${ECHO_CMD} "Deinstall slurm-wlm and run make again."; \ ${ECHO_CMD} "********************************************"; \ false; \ fi post-install: ${INSTALL_DATA} ${WRKSRC}/etc/slurm.conf.example \ ${STAGEDIR}${PREFIX}/etc/slurm.conf.sample .include