Index: head/biology/gemma/Makefile =================================================================== --- head/biology/gemma/Makefile (revision 534189) +++ head/biology/gemma/Makefile (revision 534190) @@ -1,39 +1,39 @@ # $FreeBSD$ PORTNAME= gemma DISTVERSION= 0.98.1 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Genome-wide Efficient Mixed Model Association LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libgsl.so:math/gsl USES= blaslapack:openblas compiler:c++11-lang eigen:3 gmake \ localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= genetics-statistics GH_PROJECT= GEMMA MAKEFILE= ${FILESDIR}/Makefile # Assuming openblas is built with pthreads, not openmp CXXFLAGS+= -I${LOCALBASE}/include/eigen3 -DOPENBLAS -pthread LDFLAGS+= -lopenblas -pthread OPTIONS_DEFINE= EXAMPLES pre-configure: @${REINPLACE_CMD} -e 's|../bin/gemma|../gemma|' ${WRKSRC}/test/*.sh do-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) do-test: (cd ${WRKSRC}/test && ${SH} test_suite.sh) .include Index: head/biology/plink/Makefile =================================================================== --- head/biology/plink/Makefile (revision 534189) +++ head/biology/plink/Makefile (revision 534190) @@ -1,57 +1,58 @@ # $FreeBSD$ PORTNAME= plink DISTVERSIONPREFIX= v DISTVERSION= 1.90b6.17 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Whole genome association analysis toolset LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE NOT_FOR_ARCHS= aarch64 mips64 powerpc64 sparc64 NOT_FOR_ARCHS_REASON= 64bit code requires SSE2 instructions USES= gmake fortran USE_GITHUB= yes GH_ACCOUNT= chrchang GH_PROJECT= plink-ng GH_TAGNAME= 79b2df8c WRKSRC_SUBDIR= 1.9 MAKEFILE= Makefile.std MAKE_ARGS= ZLIB=-lz BLASFLAGS="${BLASLIB} ${LAPACKLIB}" CFLAGS+= -DDYNAMIC_ZLIB -I${LOCALBASE}/include LDFLAGS+= -lthr INSTALL_TARGET= install-strip OPTIONS_DEFINE= EXAMPLES OPTIONS_SINGLE= BLAS OPTIONS_SINGLE_BLAS= NETLIB OPENBLAS OPTIONS_DEFAULT= OPENBLAS BLAS_DESC= BLAS/LAPACK implementation OPENBLAS_USES= blaslapack:openblas NETLIB_DESC= Netlib's reference NETLIB_USES= blaslapack:netlib NETLIB_LIB_DEPENDS= libcblas.so:math/cblas NETLIB_LDFLAGS= -lcblas EXAMPLES= toy.map toy.ped post-build: (cd ${WRKSRC}; ${CC} ${CFLAGS} prettify.c -o prettify) post-install: ${INSTALL_PROGRAM} ${WRKSRC}/prettify ${STAGEDIR}${PREFIX}/bin post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR} .include Index: head/databases/grass7/Makefile =================================================================== --- head/databases/grass7/Makefile (revision 534189) +++ head/databases/grass7/Makefile (revision 534190) @@ -1,206 +1,207 @@ # Created by: Mikael URANKAR and Loïc BARTOLETTI # $FreeBSD$ PORTNAME= grass PORTVERSION= 7.8.2 +PORTREVISION= 1 CATEGORIES= databases geography MASTER_SITES= https://grass.osgeo.org/%SUBDIR%/ \ http://grass.cict.fr/%SUBDIR%/ \ http://grass.fbk.eu/%SUBDIR%/ \ http://grass.gis-lab.info/%SUBDIR%/ \ http://grass.meteo.uni.wroc.pl/%SUBDIR%/ \ http://grass.polytechnic.edu.na/%SUBDIR%/ \ http://grass.unibuc.ro/%SUBDIR%/ \ http://mirrors.ibiblio.org/grass/%SUBDIR%/ \ http://pinus.gntech.ac.kr/grass/%SUBDIR%/ \ http://wgbis.ces.iisc.ernet.in/grass/%SUBDIR%/ \ http://wgrass.media.osaka-cu.ac.jp/grassh/%SUBDIR%/ MASTER_SITE_SUBDIR= grass${VER}/source PKGNAMESUFFIX= 7 MAINTAINER= lbartoletti@FreeBSD.org COMMENT= Open source Geographical Information System (GIS) LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/GPL.TXT BROKEN_sparc64= Does not configure on sparc64 BUILD_DEPENDS= ${PY_NUMPY} \ ${PYTHON_SITELIBDIR}/six.py:devel/py-six@${PY_FLAVOR} LIB_DEPENDS= libgdal.so:graphics/gdal \ libpng.so:graphics/png \ libproj.so:graphics/proj \ libtiff.so:graphics/tiff \ libfftw3.so:math/fftw3 \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libgeos.so:graphics/geos RUN_DEPENDS= ${PY_NUMPY} \ ${PYTHON_SITELIBDIR}/six.py:devel/py-six@${PY_FLAVOR} USES= blaslapack compiler:openmp fortran gl gmake gnome iconv \ jpeg perl5 pkgconfig python:3.6+ readline shebangfix tk xorg SHEBANG_GLOB= *.py SHEBANG_LANG= nviz nviz_OLD_CMD= nviz nviz_CMD= ${PREFIX}/${GRASS_INST_DIR}/bin/nviz USE_XORG= sm ice x11 xext xi xmu xrender xt USE_GL= gl glu USE_GNOME= cairo USE_WX= 3.0 WX_COMPS= wx:build python:run GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-includes=${LOCALBASE}/include \ --with-libs=${LOCALBASE}/lib \ --with-opengl-includes=${LOCALBASE}/include/ \ --with-opengl-libs=${LOCALBASE}/lib/ \ --with-freetype \ --with-freetype-includes=${LOCALBASE}/include/freetype2 \ --with-blas \ --with-lapack \ --with-cairo \ --with-readline \ --enable-largefile \ --with-wxwidgets=${WX_CONFIG} \ --with-proj-share=${LOCALBASE}/share/proj \ --with-geos=${LOCALBASE}/bin/geos-config \ --with-gdal=${LOCALBASE}/bin/gdal-config \ --with-pthread=yes \ --with-openmp SUB_FILES= pkg-message SUB_LIST= PYTHON_CMD=${PYTHON_CMD} BINARY_ALIAS= python3=${PYTHON_CMD} ALL_TARGET= default USE_LDCONFIG= ${PREFIX}/${GRASS_INST_DIR}/lib MAKE_ENV+= TARGET="${CONFIGURE_TARGET}" VER= ${PORTVERSION:R:C/\.//} PLIST_SUB= GRASS_INST_DIR="${GRASS_INST_DIR}" \ VERSION="${PORTVERSION}" VERS="${PORTVERSION:C/([0-9]+).([0-9]+)(.*)/\1.\2/}" \ VER="${VER}" MAJVER="${PKGNAMESUFFIX}" OPTIONS_DEFINE= LAS NETCDF NLS PDAL ZSTD OPTIONS_MULTI= DB OPTIONS_MULTI_DB= MYSQL ODBC PGSQL SQLITE #OPTIONS_SINGLE= BLAS #OPTIONS_SINGLE_BLAS= ATLAS NETLIB GOTOBLAS OPENBLAS OPTIONS_DEFAULT= LAS NETCDF NLS PDAL PGSQL SQLITE ZSTD OPTIONS_SUB= yes # BLAS/LAPACK: Only netlib compile the maxmimum number of modules #BLAS_DESC= BLAS/LAPACK support #GOTOBLAS_DESC= GotoBLAS implementationS #ATLAS_USES= blaslapack:atlas #NETLIB_USES= blaslapack #GOTOBLAS_USES= blaslapack:gotoblas #OPENBLAS_USES= blaslapack:openblas LAS_DESC= Enable LiDAR modules PDAL_DESC= Enable points cloud data modules DB_DESC= Database support LAS_CONFIGURE_ON= --with-liblas=yes LAS_LIB_DEPENDS= liblas.so:devel/liblas \ libboost_program_options.so:devel/boost-libs \ libboost_thread.so:devel/boost-libs \ libgeotiff.so:graphics/libgeotiff MYSQL_USES= mysql MYSQL_CONFIGURE_ON= --with-mysql \ --with-mysql-includes=${LOCALBASE}/include/mysql \ --with-mysql-libs=${LOCALBASE}/lib/mysql NETCDF_CONFIGURE_ON= --with-netcdf=${LOCALBASE}/bin/nc-config NETCDF_LIB_DEPENDS= libnetcdf.so:science/netcdf NLS_CONFIGURE_WITH= nls NLS_USES= gettext ODBC_LIB_DEPENDS= libodbc.so:databases/unixODBC ODBC_CONFIGURE_WITH= odbc PDAL_CONFIGURE_ON= --with-pdal=${LOCALBASE}/bin/pdal-config PDAL_LIB_DEPENDS= libpdal_base.so:math/pdal PGSQL_USES= pgsql PGSQL_CONFIGURE_WITH= postgres SQLITE_USES= sqlite SQLITE_CONFIGURE_WITH= sqlite SQLITE_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}sqlite3>0:databases/py-sqlite3@${PY_FLAVOR} ZSTD_CONFIGURE_WITH= zstd ZSTD_LIB_DEPENDS= libzstd.so:archivers/zstd .include .if !defined (GRASS_INST_DIR) GRASS_INST_DIR= ${PORTNAME}${VER} .endif MANDIRS= ${PREFIX}/grass${VER}/docs/man/man1 post-patch: ${REINPLACE_CMD} -e \ 's|-lblas|${BLASLIB}|g ; \ s|-llapack|${LAPACKLIB}|g ; \ s|g2c|f2c|g' ${WRKSRC}/configure ${REINPLACE_CMD} -e \ 's|make -C|$$(MAKE) -C| ; \ /^BINDIR/s|=.*|= $${DESTDIR}$${UNIX_BIN}| ; \ /test /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \ /tar /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \ /chmod /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \ /tar /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \ /rm /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \ /$$(MAKE) /s| $$(INST_DIR)| $${DESTDIR}$${INST_DIR}|g ; \ /^$$(INST_DIR)\//s|$$(INST_DIR)|$${DESTDIR}$${INST_DIR}|g ; \ s|> $$(INST_DIR)|> $${DESTDIR}$${INST_DIR}|' ${WRKSRC}/include/Make/Install.make ${REINPLACE_CMD} \ 's|= python3|= ${PYTHON_CMD:T}|' ${WRKSRC}/include/Make/Platform.make.in ${REINPLACE_CMD} \ "s|'make'|'gmake'|g" ${WRKSRC}/scripts/g.extension/g.extension.py ${REINPLACE_CMD} \ 's|$$(ARCH)|$$(TARGET)|g' ${WRKSRC}/include/Make/Grass.make # Replace hardcoded python interpreter to PYTHON_CMD ${REINPLACE_CMD} "s|'GRASS_PYTHON', 'python'|'GRASS_PYTHON', \'${PYTHON_CMD}\'|g" \ ${WRKSRC}/scripts/wxpyimgview/wxpyimgview.py ${REINPLACE_CMD} 's|GRASS_PYTHON=python|GRASS_PYTHON=${PYTHON_CMD}|g' \ ${WRKSRC}/lib/init/grass.sh ${REINPLACE_CMD} \ "s|environ\['GRASS_PYTHON'\] = "'"python3"'"|environ['GRASS_PYTHON'] = "'"${PYTHON_CMD}"'"|g" \ ${WRKSRC}/lib/python/script/setup.py post-install: # remove useless files ${RM} -rf ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/etc/db.test/ ${RM} -rf ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/demolocation/PERMANENT/.tmp/ ${RM} -rf ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/docs/html/colortables/*bak.png # fix pkg-plist issues # poudriere testport, poudriere bulk -t and make ports can create different pkg-plist for i in `${FIND} ${WRKSRC}/scripts -type f \( -name *jpg -o -name *png -o -name *gxm \) -print`; do \ ${INSTALL_DATA} $$i ${STAGEDIR}${LOCALBASE}/${PORTNAME}${VER}/docs/html; \ done for i in `${FIND} ${WRKSRC}/gui/wxpython -type f \( -name *jpg -o -name *png -o -name *gxm \) -print`; do \ ${INSTALL_DATA} $$i ${STAGEDIR}${LOCALBASE}/${PORTNAME}${VER}/docs/html; \ done for i in `${FIND} ${WRKSRC}/raster -type f \( -name *jpg -o -name *png -o -name *gxm \) -print`; do \ ${INSTALL_DATA} $$i ${STAGEDIR}${LOCALBASE}/${PORTNAME}${VER}/docs/html; \ done for i in `${FIND} ${WRKSRC}/imagery -type f \( -name *jpg -o -name *png -o -name *gxm \) -print`; do \ ${INSTALL_DATA} $$i ${STAGEDIR}${LOCALBASE}/${PORTNAME}${VER}/docs/html; \ done .for file in wms_base.py wms_drv.py wms_gdal_drv.py wms_cap_parsers.py srs.py ${INSTALL_SCRIPT} ${WRKSRC}/scripts/r.in.wms/${file} ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/etc/r.in.wms/${file} .endfor ${INSTALL_SCRIPT} ${WRKSRC}/scripts/wxpyimgview/wxpyimgview_gui.py ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/etc/wxpyimgview_gui.py ${MKDIR} ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/etc/d.polar ${INSTALL_DATA} ${WRKSRC}/scripts/d.polar/ps_defs.eps ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/etc/d.polar # STRIP PART ${STRIP_CMD} ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/bin/* ${STRIP_CMD} ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/driver/db/* .for i in clean_temp current_time_s_ms echo i.find lock run r.watershed/seg r.watershed/ram lister/vector lister/cell ${STRIP_CMD} ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/etc/${i} .endfor ${STRIP_CMD} ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/tools/g.echo ${STRIP_CMD} ${STAGEDIR}${PREFIX}/${GRASS_INST_DIR}/lib/* # symlink grass7 ${LN} -sf ${PORTNAME}${VER} \ ${STAGEDIR}${PREFIX}/bin/${PORTNAME}${PKGNAMESUFFIX} .include Index: head/mail/rspamd/Makefile =================================================================== --- head/mail/rspamd/Makefile (revision 534189) +++ head/mail/rspamd/Makefile (revision 534190) @@ -1,94 +1,94 @@ # $FreeBSD$ PORTNAME= rspamd PORTVERSION= 2.5 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= mail MAINTAINER= vsevolod@FreeBSD.org COMMENT= Fast spam filtering system LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.md LIB_DEPENDS= libpcre.so:devel/pcre \ libicui18n.so:devel/icu \ libsodium.so:security/libsodium BUILD_DEPENDS= ragel:devel/ragel RUN_DEPENDS= ca_root_nss>=3.*:security/ca_root_nss USES= cmake compiler:c11 gnome perl5 pkgconfig \ sqlite ssl USE_LDCONFIG= yes USE_PERL5= build run USE_GNOME= glib20 CONFLICTS_INSTALL= rspamd-devel USERS= rspamd GROUPS= rspamd OPTIONS_DEFINE= BLAS CGP GPERF LUAJIT OPTIONS_DEFINE_amd64= HYPERSCAN OPTIONS_DEFAULT_amd64= LUAJIT OPTIONS_DEFAULT_armv7= LUAJIT OPTIONS_DEFAULT_i386= LUAJIT OPTIONS_DEFAULT_powerpc= LUAJIT OPTIONS_SUB= yes BLAS_DESC= Use OpenBLAS to accelerate KANN CGP_DESC= Install Communigate Pro(tm) helper GPERF_DESC= Google perf-tools profiling HYPERSCAN_DESC= Use hyperscan optimizations (amd64 only) LUAJIT_DESC= Use LuaJIT instead of standard Lua SUB_FILES= pkg-message rspamd.newsyslog.conf.sample PLIST_SUB+= ETCDIR=etc/rspamd \ RSPAMDVERSION=${PORTVERSION} CMAKE_ARGS+= -DCONFDIR=${PREFIX}/etc/rspamd \ -DLOGDIR=/var/log/rspamd \ -DDBDIR=/var/db/rspamd \ -DRUNDIR=/var/run/rspamd \ -DMANDIR=${MANPREFIX}/man \ -DCMAKE_INSTALL_PREFIX=${PREFIX} \ -DBUILD_PORT=yes \ -DLIBDIR=${PREFIX}/lib/rspamd USE_GITHUB= yes USE_RC_SUBR= rspamd BLAS_CMAKE_ON= -DENABLE_BLAS=ON BLAS_USES= blaslapack:openblas GPERF_CMAKE_ON= -DENABLE_GPERF_TOOLS=ON GPERF_LIB_DEPENDS= libprofiler.so:devel/google-perftools HYPERSCAN_CMAKE_ON= -DENABLE_HYPERSCAN=ON HYPERSCAN_LIB_DEPENDS= libhs.so:devel/hyperscan LUAJIT_LIB_DEPENDS= libluajit-5.1.so:lang/luajit LUAJIT_USES_OFF= lua:51 CGP_RUN_DEPENDS+= \ p5-AnyEvent-HTTP>=0:www/p5-AnyEvent-HTTP \ p5-AnyEvent>=0:devel/p5-AnyEvent \ p5-EV>=0:devel/p5-EV \ p5-JSON-XS>=0:converters/p5-JSON-XS post-install: @${MKDIR} \ ${STAGEDIR}/var/log/rspamd \ ${STAGEDIR}/var/db/rspamd \ ${STAGEDIR}/var/run/rspamd ${RM} ${STAGEDIR}/${ETCDIR}/rspamd.conf.sample # Linux specific ${RM} ${STAGEDIR}/${ETCDIR}/rspamd.systemd.conf ${RM} ${STAGEDIR}/${ETCDIR}/rspamd.sysvinit.conf ${INSTALL_DATA} ${WRKDIR}/rspamd.newsyslog.conf.sample ${STAGEDIR}${ETCDIR} @${MKDIR} ${STAGEDIR}${PREFIX}/etc/newsyslog.conf.d ${LN} -s ${ETCDIR}/rspamd.newsyslog.conf ${STAGEDIR}${PREFIX}/etc/newsyslog.conf.d post-install-CGP-on: ${INSTALL_SCRIPT} ${WRKSRC}/utils/cgp_rspamd.pl ${STAGEDIR}${PREFIX}/bin/rspamd-cgp-helper .include Index: head/mail/rspamd-devel/Makefile =================================================================== --- head/mail/rspamd-devel/Makefile (revision 534189) +++ head/mail/rspamd-devel/Makefile (revision 534190) @@ -1,99 +1,99 @@ # $FreeBSD$ PORTNAME= rspamd PORTVERSION= 2.6.a1.20200402 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= mail PKGNAMESUFFIX= -devel MAINTAINER= vsevolod@FreeBSD.org COMMENT= Fast spam filtering system dev version LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.md LIB_DEPENDS= libpcre.so:devel/pcre \ libicui18n.so:devel/icu \ libsodium.so:security/libsodium BUILD_DEPENDS= ragel:devel/ragel RUN_DEPENDS= ca_root_nss>=3.*:security/ca_root_nss USES= cmake compiler:c11 gnome perl5 pkgconfig \ sqlite ssl USE_LDCONFIG= yes USE_PERL5= build run USE_GNOME= glib20 CONFLICTS_INSTALL= rspamd USERS= rspamd GROUPS= rspamd OPTIONS_DEFINE= BLAS CGP GPERF LUAJIT OPTIONS_DEFINE_amd64= HYPERSCAN OPTIONS_DEFAULT_amd64= LUAJIT OPTIONS_DEFAULT_armv7= LUAJIT OPTIONS_DEFAULT_i386= LUAJIT OPTIONS_DEFAULT_powerpc= LUAJIT OPTIONS_SUB= yes BLAS_DESC= Use OpenBLAS to accelerate KANN CGP_DESC= Install Communigate Pro(tm) helper GPERF_DESC= Google perf-tools profiling HYPERSCAN_DESC= Use hyperscan optimizations (amd64 only) LUAJIT_DESC= Use LuaJIT instead of standard Lua SUB_FILES= pkg-message rspamd.newsyslog.conf.sample PLIST_SUB+= ETCDIR=etc/rspamd \ RSPAMDVERSION=${PORTVERSION:C/^([^.]+\.[^.]+).*/\1/} CMAKE_ARGS+= -DCONFDIR=${PREFIX}/etc/rspamd \ -DLOGDIR=/var/log/rspamd \ -DDBDIR=/var/db/rspamd \ -DRUNDIR=/var/run/rspamd \ -DMANDIR=${MANPREFIX}/man \ -DCMAKE_INSTALL_PREFIX=${PREFIX} \ -DBUILD_PORT=yes \ -DLIBDIR=${PREFIX}/lib/rspamd \ -DDEBUG=ON \ -DGIT_ID=${GH_TAGNAME} USE_GITHUB= yes GH_TAGNAME= 76a1fb0 DEBUG_FLAGS= -g -O0 USE_RC_SUBR= rspamd BLAS_CMAKE_ON= -DENABLE_BLAS=ON BLAS_USES= blaslapack:openblas GPERF_CMAKE_ON= -DENABLE_GPERF_TOOLS=ON GPERF_LIB_DEPENDS= libprofiler.so:devel/google-perftools HYPERSCAN_CMAKE_ON= -DENABLE_HYPERSCAN=ON HYPERSCAN_LIB_DEPENDS= libhs.so:devel/hyperscan LUAJIT_LIB_DEPENDS= libluajit-5.1.so:lang/luajit LUAJIT_USES_OFF= lua:51 CGP_RUN_DEPENDS+= \ p5-AnyEvent-HTTP>=0:www/p5-AnyEvent-HTTP \ p5-AnyEvent>=0:devel/p5-AnyEvent \ p5-EV>=0:devel/p5-EV \ p5-JSON-XS>=0:converters/p5-JSON-XS post-install: @${MKDIR} \ ${STAGEDIR}/var/log/rspamd \ ${STAGEDIR}/var/db/rspamd \ ${STAGEDIR}/var/run/rspamd ${RM} ${STAGEDIR}/${ETCDIR}/rspamd.conf.sample # Linux specific ${RM} ${STAGEDIR}/${ETCDIR}/rspamd.systemd.conf ${RM} ${STAGEDIR}/${ETCDIR}/rspamd.sysvinit.conf ${INSTALL_DATA} ${WRKDIR}/rspamd.newsyslog.conf.sample ${STAGEDIR}${ETCDIR} @${MKDIR} ${STAGEDIR}${PREFIX}/etc/newsyslog.conf.d ${LN} -s ${ETCDIR}/rspamd.newsyslog.conf ${STAGEDIR}${PREFIX}/etc/newsyslog.conf.d post-install-CGP-on: ${INSTALL_SCRIPT} ${WRKSRC}/utils/cgp_rspamd.pl ${STAGEDIR}${PREFIX}/bin/rspamd-cgp-helper .include Index: head/math/R/Makefile =================================================================== --- head/math/R/Makefile (revision 534189) +++ head/math/R/Makefile (revision 534190) @@ -1,152 +1,153 @@ # Created by: Maurice Castro # $FreeBSD$ PORTNAME= R DISTVERSION= 4.0.0 +PORTREVISION= 1 CATEGORIES= math lang MASTER_SITES= CRAN/src/base/R-${PORTVERSION:C|\..*||} MAINTAINER= jrm@FreeBSD.org COMMENT= Language for statistical computing and graphics LICENSE= GPLv2 ONLY_FOR_ARCHS= aarch64 amd64 armv6 armv7 i386 powerpc64 BUILD_DEPENDS= texi2any:print/texinfo LIB_DEPENDS= libcurl.so:ftp/curl \ libpcre2-8.so:devel/pcre2 RUN_DEPENDS= gmake:devel/gmake # R packages may require GNU make # possible TODO # - Use --with-recommended-packages=no by default # - Add an option for recommended packages # - Create ports for each of the recommended packages # - Create a meta-port for the recommended packages USES= compiler:c++11-lang gmake iconv libtool localbase pathfix perl5 \ readline:port USE_LDCONFIG= ${PREFIX}/lib/R/lib USE_PERL5= build GNU_CONFIGURE= yes CONFIGURE_ARGS= --disable-java \ --enable-R-shlib \ --with-readline \ rdocdir=${DOCSDIR} INSTALL_TARGET= install-strip PLIST_SUB= FULLVER=${DISTVERSION} MAJORVER=${_MAJORVER} OPTIONS_DEFINE= ICU INFO LDOUBLE LETTER MEMPROF NLS RPROF X11 OPTIONS_DEFINE_amd64= FLANG OPENMP OPTIONS_DEFINE_i386= OPENMP OPTIONS_DEFAULT= CAIROPANGO GHOSTSCRIPT ICU INFO JPEG LDOUBLE PNG RBLAS \ RPROF TCLTK TIFF X11 OPTIONS_DEFAULT_amd64= OPENMP OPTIONS_DEFAULT_i386= OPENMP OPTIONS_GROUP= NEEDX11 OPTIONS_GROUP_NEEDX11= CAIROPANGO GHOSTSCRIPT JPEG PNG TCLTK TEXDOCS TIFF OPTIONS_SINGLE= BLAS OPTIONS_SINGLE_BLAS= ATLAS NETLIB OPENBLAS RBLAS OPTIONS_SUB= YES ATLAS_DESC= ATLAS BLAS implementation CAIROPANGO_DESC= Cairo graphics device and Pango multi-language text FLANG_DESC= Use experimental flang Fortran compiler GHOSTSCRIPT_DESC= Graphics device for bitmap files via Ghostscript JPEG_DESC= JPEG graphics device LDOUBLE_DESC= Long double data type LETTER_DESC= US letter paper MEMPROF_DESC= Memory profiling via Rprofmem() and tracemem() NEEDX11_DESC= Require X11 NETLIB_DESC= Netlib BLAS implementation OPENBLAS_DESC= OpenBLAS BLAS implementation PNG_DESC= PNG graphics device RBLAS_DESC= Use R-bundled BLAS implementation RPROF_DESC= R profiling via Rprof() TEXDOCS_DESC= Build/Install TeX-dependent documentation files X11_DESC= X11 graphics device ATLAS_USES= blaslapack:atlas ATLAS_CONFIGURE_ON= --disable-BLAS-shlib CAIROPANGO_IMPLIES= X11 CAIROPANGO_USES= gettext gnome jpeg pkgconfig CAIROPANGO_USE= GNOME=cairo,pango CAIROPANGO_CONFIGURE_WITH= cairo FLANG_PREVENTS= ATLAS NETLIB OPENBLAS FLANG_LIB_DEPENDS= libpgmath.so:math/libpgmath FLANG_USES= fortran:flang GHOSTSCRIPT_IMPLIES= X11 GHOSTSCRIPT_USES= ghostscript ICU_LIB_DEPENDS= libicui18n.so:devel/icu ICU_CONFIGURE_WITH= ICU INFO_INSTALL_TARGET= install-info INFO_INFO= R-admin R-data R-exts R-FAQ R-intro R-ints \ R-lang JPEG_IMPLIES= X11 JPEG_USES= jpeg pkgconfig JPEG_CONFIGURE_WITH= jpeglib JPEG_CONFIGURE_ENV= r_cv_header_jpeglib_h=yes LDOUBLE_CONFIGURE_ENABLE= long-double LETTER_CONFIGURE_ENV= R_PAPERSIZE=letter MEMPROF_CONFIGURE_ENABLE= memory-profiling NETLIB_USES= blaslapack:netlib NETLIB_CONFIGURE_ON= --disable-BLAS-shlib NLS_USES= gettext NLS_CONFIGURE_OFF= --disable-nls OPENBLAS_USES= blaslapack:openblas OPENBLAS_CONFIGURE_ON= --disable-BLAS-shlib OPENMP_CONFIGURE_ENABLE= openmp PNG_IMPLIES= X11 PNG_LIB_DEPENDS= libpng.so:graphics/png PNG_CONFIGURE_WITH= libpng RBLAS_CONFIGURE_ON= --enable-BLAS-shlib \ --without-blas \ --without-lapack RBLAS_CONFIGURE_OFF= --with-blas="-L${LOCALBASE}/lib ${BLASLIB}" \ --with-lapack="${LAPACKLIB}" RBLAS_EXTRA_PATCHES= ${PATCHDIR}/extra-patch-src_extra_blas_Makefile.in \ ${PATCHDIR}/extra-patch-src_modules_lapack_Makefile.in RPROF_CONFIGURE_ENABLE= R-profiling TCLTK_IMPLIES= X11 TCLTK_USES= tcl tk TCLTK_CONFIGURE_WITH= tcltk TEXDOCS_USE= TEX=dvipsk:build,kpathsea:build,pdftex:build .for i in KPSEWHICH MAKEINDEX PDFLATEX PDFTEX TEX TEXI2DVI TEXDOCS_CONFIGURE_ENV_OFF+= ac_cv_path_${i}="" .endfor TEXDOCS_INSTALL_TARGET= install-pdf TIFF_IMPLIES= X11 TIFF_LIB_DEPENDS= libtiff.so:graphics/tiff TIFF_CONFIGURE_WITH= libtiff X11_USES= xorg X11_USE= XORG=ice,sm,x11,xext,xmu,xscrnsaver,xt X11_CONFIGURE_WITH= x _MAJORVER= ${DISTVERSION:R:R} .include .if ! ${PORT_OPTIONS:MFLANG} USES+= fortran .endif post-patch: @${REINPLACE_CMD} -e "s|/usr/local|${LOCALBASE}|g" ${WRKSRC}/configure @${REINPLACE_CMD} \ -e "s|%%FULLVER%%|${DISTVERSION}|" \ -e "s|%%MAJORVER%%|${_MAJORVER}|" \ ${WRKSRC}/src/main/Makefile.in \ ${WRKSRC}/src/extra/blas/Makefile.in \ ${WRKSRC}/src/modules/lapack/Makefile.in post-install-RBLAS-off: @${REINPLACE_CMD} -e "s| -lR| -lR ${BLASLIB}|" \ ${STAGEDIR}${PREFIX}/libdata/pkgconfig/libR.pc post-install-RBLAS-on: @${REINPLACE_CMD} -e "s| -lR| -lR -lRblas|" \ ${STAGEDIR}${PREFIX}/libdata/pkgconfig/libR.pc .include Index: head/math/adept/Makefile =================================================================== --- head/math/adept/Makefile (revision 534189) +++ head/math/adept/Makefile (revision 534190) @@ -1,34 +1,34 @@ # $FreeBSD$ PORTNAME= adept DISTVERSION= 2.0.5 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= math MASTER_SITES= http://www.met.reading.ac.uk/clouds/adept/ MAINTAINER= yuri@FreeBSD.org COMMENT= Combined array and automatic differentiation library in C++ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/COPYING USES= autoreconf gmake fortran blaslapack:openblas libtool GNU_CONFIGURE= yes CONFIGURE_ARGS= --disable-static USE_LDCONFIG= yes INSTALL_TARGET= install-strip OPTIONS_DEFINE= PDFTEXDOCS PDFTEXDOCS_DESC= Build and install PDF documentation from LaTeX sources OPTIONS_SUB= yes PDFTEXDOCS_USE= TEX=pdftex:build,dvipsk:build post-build-PDFTEXDOCS-on: @cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} post-install-PDFTEXDOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/doc/*.pdf ${STAGEDIR}${DOCSDIR} .include Index: head/math/casadi/Makefile =================================================================== --- head/math/casadi/Makefile (revision 534189) +++ head/math/casadi/Makefile (revision 534190) @@ -1,71 +1,71 @@ # $FreeBSD$ PORTNAME= casadi DISTVERSION= 3.5.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Symbolic framework for numeric optimization LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt USES= cmake compiler:c++11-lang pkgconfig USE_GITHUB= yes USE_LDCONFIG= yes CFLAGS+= -fPIC CXXFLAGS+= -fPIC CMAKE_OFF= WITH_DEEPBIND WITH_BUILD_BLASFEO # cmake-3.16: disable build of examples (they are not installed anyways), # and fail due to not setting up the linker environment properly: CMAKE_OFF+= WITH_EXAMPLES OPTIONS_DEFINE= BLASFEO BONMIN CLANG IPOPT LAPACK QPOASES OPTIONS_DEFAULT= BLASFEO BONMIN IPOPT LAPACK QPOASES OPTIONS_SUB= yes BLASFEO_DESC= Build with BLASFEO BLASFEO_CMAKE_BOOL= WITH_BLASFEO BLASFEO_BUILD_DEPENDS= blasfeo>0:math/blasfeo BONMIN_DESC= Build with Bonmin BONMIN_CMAKE_BOOL= WITH_BONMIN BONMIN_USES= blaslapack:netlib fortran BONMIN_LIB_DEPENDS= libbonmin.so:math/bonmin \ libCbcSolver.so:math/coinmp \ libipopt.so:math/ipopt CLANG_DESC= Build with clang for JIT CLANG_CMAKE_BOOL= WITH_CLANG CLANG_BROKEN= Fails to find clang IPOPT_DESC= Build with IPopt IPOPT_CMAKE_BOOL= WITH_IPOPT IPOPT_USES= blaslapack:netlib fortran IPOPT_LIB_DEPENDS= libipopt.so:math/ipopt LAPACK_DESC= Build with LAPACK LAPACK_CMAKE_BOOL= WITH_LAPACK LAPACK_USES= blaslapack:openblas QPOASES_DESC= Build with qpOASES QPOASES_CMAKE_BOOL= WITH_QPOASES QPOASES_LIB_DEPENDS= libopenblas.so:math/openblas QPOASES_IMPLIES= LAPACK .include .if ${PORT_OPTIONS:MCLANG} # use clang from ports because cmake can't find base llvm for JIT BUILD_DEPENDS+= clang${LLVM_DEFAULT}:devel/llvm${LLVM_DEFAULT} RUN_DEPENDS+= clang${LLVM_DEFAULT}:devel/llvm${LLVM_DEFAULT} CPP= clang-cpp${LLVM_DEFAULT} CC= clang${LLVM_DEFAULT} CXX= clang++${LLVM_DEFAULT} .endif .include Index: head/math/ceres-solver/Makefile =================================================================== --- head/math/ceres-solver/Makefile (revision 534189) +++ head/math/ceres-solver/Makefile (revision 534190) @@ -1,120 +1,120 @@ # $FreeBSD$ PORTNAME= ceres-solver DISTVERSION= 1.14.0 -PORTREVISION= 17 +PORTREVISION= 18 CATEGORIES= math MAINTAINER= jbeich@FreeBSD.org COMMENT= Nonlinear least squares minimizer LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libglog.so:devel/glog RUN_DEPENDS:= ${BUILD_DEPENDS:Meigen*} USES= cmake compiler:${OPENMP}c++11-lib eigen:3 localbase shebangfix USE_GITHUB= yes USE_LDCONFIG= yes SHEBANG_FILES= examples/slam/pose_graph_*/plot_results.py \ scripts/make_docs.py CMAKE_ON= CXX11 BUILD_SHARED_LIBS CMAKE_OFF= BUILD_BENCHMARKS LDFLAGS+= -Wl,--as-needed # -lccolamd -lcholmod -lrt from suitesparse PLIST_SUB= VERSION=${DISTVERSION:C/rc.*//} EXAMPLESDIR= ${PREFIX}/share/examples/${PORTNAME:S/-solver//} DOCSDIR= ${PREFIX}/share/doc/${PORTNAME:S/-solver//} PORTDOCS= * PORTEXAMPLES= * OPTIONS_DEFINE= CUSTOM_BLAS EXAMPLES DOCS GFLAGS LAPACK SCHUR TEST OPTIONS_DEFAULT=CUSTOM_BLAS CXSPARSE OPENBLAS OPENMP SCHUR SUITESPARSE OPTIONS_RADIO= LAPACK THREADS OPTIONS_RADIO_LAPACK= ATLAS GOTOBLAS NETLIB OPENBLAS OPTIONS_RADIO_THREADS= OPENMP TBB OPTIONS_GROUP= SPARSE OPTIONS_GROUP_SPARSE= CXSPARSE EIGENSPARSE SUITESPARSE CUSTOM_BLAS_DESC= Handcoded BLAS routines instead of Eigen CUSTOM_BLAS_CMAKE_BOOL= CUSTOM_BLAS DOCS_BUILD_DEPENDS= sphinx-build:textproc/py-sphinx DOCS_USES= python:build DOCS_CMAKE_BOOL= BUILD_DOCUMENTATION EXAMPLES_CMAKE_BOOL= BUILD_EXAMPLES EXAMPLES_IMPLIES= GFLAGS GFLAGS_DESC= Google Flags support GFLAGS_LIB_DEPENDS= libgflags.so:devel/gflags GFLAGS_CMAKE_BOOL= GFLAGS OPENMP_USES= compiler:openmp OPENMP_CMAKE_BOOL= OPENMP .if !exists(/usr/include/omp.h) # XXX ports/199603: LLVM openmp in base doesn't support aarch64, armv6, armv7 yet OPENMP_VARS= OPENMP=gcc- .endif SCHUR_DESC= Fixed-size schur specializations SCHUR_CMAKE_BOOL= SCHUR_SPECIALIZATIONS TBB_DESC= Intel threading building blocks TBB_LIB_DEPENDS= libtbb.so:devel/tbb TBB_CMAKE_BOOL= TBB # XXX Unbundle googletest/googlemock TEST_CMAKE_BOOL= BUILD_TESTING TEST_TEST_TARGET= test TEST_IMPLIES= GFLAGS LAPACK_DESC= Linear Algebra PACKage LAPACK_CMAKE_BOOL= LAPACK # Avoid conflict with Ceres threading by using single-threaded BLAS library. # BLASLIB from USES=blaslapack cannot be used as it's multi-threaded. # https://github.com/xianyi/OpenBLAS/wiki/faq#multi-threaded ATLAS_USES= blaslapack:atlas ATLAS_CMAKE_ON= -DBLA_VENDOR:STRING="ATLAS" \ -DBLAS_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libcblas.so" \ -DLAPACK_LIBRARIES:FILEPATH="${LOCALBASE}/lib/libalapack.so" ATLAS_IMPLIES= LAPACK GOTOBLAS_DESC= Goto blas implementation GOTOBLAS_USES= blaslapack:gotoblas GOTOBLAS_CMAKE_ON= -DBLA_VENDOR:STRING="Goto" GOTOBLAS_IMPLIES= LAPACK NETLIB_USES= blaslapack:netlib NETLIB_CMAKE_ON= -DBLA_VENDOR:STRING="Generic" NETLIB_IMPLIES= LAPACK OPENBLAS_USES= blaslapack:openblas OPENBLAS_CMAKE_ON= -DBLA_VENDOR:STRING="OpenBLAS" OPENBLAS_IMPLIES= LAPACK SPARSE_DESC= Sparse linear algebra library CXSPARSE_DESC= CXSparse support CXSPARSE_LIB_DEPENDS= libcxsparse.so:math/suitesparse CXSPARSE_CMAKE_ON= -DCXSPARSE_INCLUDE_DIR:PATH="${LOCALBASE}/include/suitesparse" CXSPARSE_CMAKE_BOOL= CXSPARSE EIGENSPARSE_DESC= Simplicial Cholesky factorization in Eigen EIGENSPARSE_CMAKE_BOOL= EIGENSPARSE EIGENSPARSE_VARS= LICENSE+=LGPL21+ LICENSE_COMB=multi \ LICENSE_FILE_BSD3CLAUSE="${LICENSE_FILE}" SUITESPARSE_DESC= SuiteSparse support SUITESPARSE_LIB_DEPENDS=libspqr.so:math/suitesparse SUITESPARSE_CMAKE_BOOL= SUITESPARSE post-patch-DOCS-on: @${REINPLACE_CMD} -e 's,python,${PYTHON_CMD:T},' \ ${WRKSRC}/docs/source/CMakeLists.txt pre-install-TEST-on: do-test post-install-EXAMPLES-on: # Copy examples (stripped), their source and sample data but not tests programs (cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR}) (cd ${WRKSRC} && ${COPYTREE_SHARE} data ${STAGEDIR}${EXAMPLESDIR}) (cd ${BUILD_WRKSRC} && ${COPYTREE_SHARE} bin ${STAGEDIR}${EXAMPLESDIR}) @${RM} -r ${STAGEDIR}${EXAMPLESDIR}/bin/*_test -@${STRIP_CMD} ${STAGEDIR}${EXAMPLESDIR}/bin/* # may fail for non-root .include Index: head/math/cminpack/Makefile =================================================================== --- head/math/cminpack/Makefile (revision 534189) +++ head/math/cminpack/Makefile (revision 534190) @@ -1,29 +1,29 @@ # $FreeBSD$ PORTNAME= cminpack PORTVERSION= 1.3.6 DISTVERSIONPREFIX= v -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math MAINTAINER= fernape@FreeBSD.org COMMENT= Solving nonlinear equations and nonlinear least squares problems LICENSE_FILE= ${WRKSRC}/CopyrightMINPACK.txt USES= blaslapack:openblas cmake localbase USE_GITHUB= yes GH_ACCOUNT= devernay CMAKE_ON= BUILD_SHARED_LIBS CMAKE_OFF= USE_BLAS OPTIONS_DEFINE= EXAMPLES post-install-EXAMPLES-on: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKSRC}/examples/ && ${COPYTREE_SHARE} "*.[ch] testdata" \ ${STAGEDIR}${EXAMPLESDIR}) .include Index: head/math/dbcsr/Makefile =================================================================== --- head/math/dbcsr/Makefile (revision 534189) +++ head/math/dbcsr/Makefile (revision 534190) @@ -1,48 +1,48 @@ # $FreeBSD$ PORTNAME= dbcsr DISTVERSIONPREFIX= v DISTVERSION= 2.0.1 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Distributed Block Compressed Sparse Row matrix library LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= fypp:devel/py-fypp@${PY_FLAVOR} USES= blaslapack:openblas cmake:noninja compiler:c++14-lang fortran \ python:build USE_GITHUB= yes GH_ACCOUNT= cp2k USE_LDCONFIG= yes LDFLAGS+= -lopenblas CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DBLA_VENDOR:STRING="OpenBLAS" TEST_TARGET= test # tests hang: https://github.com/cp2k/dbcsr/issues/72 OPTIONS_DEFINE= MPI OPENMP C_API # libxsmm is supposed to be supported, but cmake build lacks the corresponding option: https://github.com/cp2k/dbcsr/issues/73 OPTIONS_DEFAULT= MPI OPENMP C_API OPTIONS_SUB= yes MPI_CMAKE_BOOL= USE_MPI MPI_LIB_DEPENDS= libmpi.so:net/openmpi OPENMP_CMAKE_BOOL= USE_OPENMP C_API_DESC= Build the C API library C_API_CMAKE_BOOL= WITH_C_API do-test: # tests are broken: https://github.com/cp2k/dbcsr/issues/150 @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} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include Index: head/math/fflas-ffpack/Makefile =================================================================== --- head/math/fflas-ffpack/Makefile (revision 534189) +++ head/math/fflas-ffpack/Makefile (revision 534190) @@ -1,46 +1,47 @@ # Created by: b.f. # $FreeBSD$ PORTNAME= fflas-ffpack PORTVERSION= 2.4.3 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= ports@FreeBSD.org COMMENT= Library for dense linear algebra over word-size finite fields LICENSE= LGPL21 BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libgmp.so:math/gmp \ libgivaro.so:math/givaro RUN_DEPENDS= bash:shells/bash USE_GITHUB= yes GH_ACCOUNT= linbox-team USES= autoreconf blaslapack:openblas compiler:c++11-lang gmake \ libtool localbase pkgconfig shebangfix GNU_CONFIGURE= yes SHEBANG_FILES= fflas-ffpack-config.in TEST_TARGET= check OPTIONS_DEFINE= DOXYGEN .include .if ${PORT_OPTIONS:MDOXYGEN} BUILD_DEPENDS+= doxygen:devel/doxygen CONFIGURE_ARGS+= --enable-doc --with-docdir="${DOCSDIR}" PLIST_SUB+= DOXYGEN="" .else PLIST_SUB+= DOXYGEN="@comment " .endif post-patch-DOXYGEN-on: ${REINPLACE_CMD} -e 's/sed -i/& ""/' ${WRKSRC}/doc/Makefile.am post-install-DOXYGEN-on: @${MKDIR} ${STAGEDIR}${DOCSDIR}/fflas-ffpack-dev-html @${TOUCH} ${STAGEDIR}${DOCSDIR}/fflas-ffpack-dev-html/.keep-me .include Index: head/math/iml/Makefile =================================================================== --- head/math/iml/Makefile (revision 534189) +++ head/math/iml/Makefile (revision 534190) @@ -1,24 +1,25 @@ # Created by: thierry@pompo.net # $FreeBSD$ PORTNAME= iml PORTVERSION= 1.0.5 +PORTREVISION= 1 CATEGORIES= math MASTER_SITES= http://www.cs.uwaterloo.ca/~astorjoh/ MAINTAINER= thierry@FreeBSD.org COMMENT= Integer Matrix Library LICENSE= GPLv2 LIB_DEPENDS= libgmp.so:math/gmp USES= blaslapack:openblas libtool localbase tar:bz2 GNU_CONFIGURE= yes CONFIGURE_ARGS= --with-cblas=${LAPACKLIB} --enable-shared USE_LDCONFIG= yes TEST_TARGET= check .include Index: head/math/jags/Makefile =================================================================== --- head/math/jags/Makefile (revision 534189) +++ head/math/jags/Makefile (revision 534190) @@ -1,90 +1,90 @@ # Created by: Eric van Gyzen # $FreeBSD$ PORTNAME= mcmc-jags DISTVERSION= 4.3.0 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= math MASTER_SITES= SF/mcmc-jags/JAGS/${S}.x/Source/:1 \ SF/mcmc-jags/Examples/${S}.x/:2 \ SF/mcmc-jags/Manuals/2.x/:3 \ SF/mcmc-jags/Manuals/${S}.x/:4 DISTFILES= JAGS-${PORTVERSION}${EXTRACT_SUFX}:1 DIST_SUBDIR= ${PORTNAME} EXTRACT_ONLY= ${DISTFILES:M*[12]:C|:.*||} MAINTAINER= ports@FreeBSD.org COMMENT= Just Another Gibbs Sampler LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libltdl.so:devel/libltdl GNU_CONFIGURE= yes USES= bison compiler:features fortran gmake libtool localbase pathfix USE_GCC= yes USE_LDCONFIG= yes INSTALL_TARGET= install-strip WRKSRC= ${WRKDIR}/JAGS-${PORTVERSION} OPTIONS_SINGLE= BLAS OPTIONS_SINGLE_BLAS= ATLAS OPENBLAS NETLIB OPTIONS_DEFAULT+= OPENBLAS ATLAS_USES= blaslapack:atlas ATLAS_VARS= MANUAL_PACKAGE_BUILD=\ "Choose a BLAS option other than ATLAS for package building." NETLIB_USES= blaslapack:netlib OPENBLAS_USES= blaslapack:openblas DOCS_DISTFILES= jags_developer_manual.pdf:3 jags_installation_manual.pdf:4 \ jags_user_manual.pdf:4 DOCS_PORTDOCS= ${DISTFILES:M*[34]:C|:.*||} EXAMPLES_DISTFILES= classic-bugs.tar.gz:2 EXAMPLES_PORTEXAMPLES= * CONFIGURE_ARGS+= --with-blas="-L${LOCALBASE}/lib ${BLASLIB}" \ --with-lapack="${LAPACKLIB}" OPTIONS_SUB= YES PLIST_SUB= MODULEVERSION=${S} S= ${PORTVERSION:C|\..*||} OPTIONS_DEFINE= DOCS EXAMPLES post-patch: @${REINPLACE_CMD} \ -e '/@WINDOWS_FALSE@bin_SCRIPTS =/s/jags/mcmc-&/' \ -e '/CLEANFILES =/s/jags/mcmc-&/' \ -e '/@WINDOWS_FALSE@jags:/s/jags/mcmc-&/' \ -e '/@WINDOWS_FALSE@.*rm -f jags/s/jags/mcmc-&/' \ -e '/@WINDOWS_FALSE@.*mv jags.tmp jags/s/jags/mcmc-&/2' \ ${WRKSRC}/src/terminal/Makefile.in post-patch-EXAMPLES-on: @${SED} -i '' -e '\|JAGS ?=|{s|jags|mcmc-&|;s|/usr/local|${PREFIX}|;}' \ ${WRKDIR}/classic-bugs/vol[12]/Makefile post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} @cd ${_DISTDIR}; ${INSTALL_DATA} ${PORTDOCS} ${STAGEDIR}${DOCSDIR} post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} @cd ${WRKDIR}/classic-bugs; ${COPYTREE_SHARE} \* ${STAGEDIR}${EXAMPLESDIR} .if defined(MAINTAINER_MODE) BUILD_DEPENDS+= ${LOCALBASE}/lib/R/library/coda/R/coda.rdb:math/R-cran-coda check test: install .for i in 1 2 @cd ${WRKDIR}/classic-bugs/vol${i}; ${SETENV} ${MAKE_ENV} \ ${MAKE_CMD} ${MAKE_ARGS} check .endfor @${FIND} ${WRKDIR}/classic-bugs -type f -name check.log | ${SORT} | \ ${XARGS} -tI @ ${CAT} @ .endif .include Index: head/math/lapack++/Makefile =================================================================== --- head/math/lapack++/Makefile (revision 534189) +++ head/math/lapack++/Makefile (revision 534190) @@ -1,47 +1,47 @@ # Created by: NAKATA Maho # $FreeBSD$ PORTNAME= lapack++ PORTVERSION= 2.5.4 -PORTREVISION= 9 +PORTREVISION= 10 CATEGORIES= math MASTER_SITES= SF/lapackpp \ http://math.nist.gov/lapack++/:doc DISTNAME= lapackpp-${PORTVERSION} DIST_SUBDIR= lapackpp EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} DISTFILES= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= fortran@FreeBSD.org COMMENT= Linear Algebra PACKage in C++, a wrapper for LAPACK USES= fortran gmake pathfix libtool OPTIONS_DEFINE= DOCS OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= OPENBLAS NETLIB ATLAS OPTIONS_DEFAULT= OPENBLAS OPENBLAS_USES= blaslapack:openblas NETLIB_USES= blaslapack:netlib ATLAS_USES= blaslapack:atlas GNU_CONFIGURE= yes USE_LDCONFIG= yes BLAS_LIB= -L${LOCALBASE}/lib ${BLASLIB} LAPACK_LIB= -L${LOCALBASE}/lib ${LAPACKLIB} #lapack++ forces to use atlas when detected, so we should disable here. CONFIGURE_ARGS+= --with-blas="${BLAS_LIB}" --with-lapack="${LAPACK_LIB}" --disable-atlas --enable-static DOCS_DISTFILES= lapack++.ps.gz:doc lapackpp1_1.ps.gz:doc lapackppman1_1.ps.gz:doc lapack++_install.ps.gz:doc post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/lapack++.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/lapack++_install.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/lapackpp1_1.ps.gz ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${DIST_SUBDIR}/lapackppman1_1.ps.gz ${STAGEDIR}${DOCSDIR} .include Index: head/math/levmar/Makefile =================================================================== --- head/math/levmar/Makefile (revision 534189) +++ head/math/levmar/Makefile (revision 534190) @@ -1,73 +1,73 @@ # Created by: Eijiro Shibusawa # $FreeBSD$ PORTNAME= levmar PORTVERSION= 2.6 -PORTREVISION= 13 +PORTREVISION= 14 CATEGORIES= math MASTER_SITES= http://users.ics.forth.gr/~lourakis/levmar/ MAINTAINER= phd_kimberlite@yahoo.co.jp COMMENT= GPL-licensed library implementing the Levenberg-Marquardt algorithm LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE USE_LDCONFIG= yes USES= fortran tar:tgz uidfix OPTIONS_DEFINE= DOCS EXAMPLES PROFILE OPTIONS_SINGLE= BLASLIB OPTIONS_DEFAULT= NETLIB OPTIONS_SINGLE_BLASLIB= ATLAS NETLIB OPENBLAS PROFILE_DESC= Build a profiling library ATLAS_USES= blaslapack:atlas NETLIB_USES= blaslapack:netlib OPENBLAS_USES= blaslapack:openblas .include PORTDOCS= README.txt PORTEXAMPLES= lmdemo.c Makefile.demo PLIST_FILES= include/levmar.h \ lib/liblevmar.a \ lib/liblevmar.so \ lib/liblevmar.so.2 .if ${PORT_OPTIONS:MPROFILE} .if defined(NOPROFILE) || defined(NO_PROFILE) || defined(WITHOUT_PROFILE) IGNORE= you have defined WITH_PROFILE, but have also defined\ WITHOUT_PROFILE, NOPROFILE, or NO_PROFILE .elif !exists(/usr/lib/libc_p.a) IGNORE= you have chosen WITH_PROFILE, but have not installed the\ base system profiling libraries .endif PLIST_FILES+= lib/liblevmar_p.a .else MAKE_ENV+= WITHOUT_PROFILE=true .endif post-extract: @${MV} ${WRKSRC}/Makefile ${WRKSRC}/Makefile.dist @${CP} ${FILESDIR}/Makefile.lib ${WRKSRC}/Makefile @${CP} ${FILESDIR}/Makefile.demo ${WRKSRC}/ @${REINPLACE_CMD} -e 's+%%CC%%+${CC}+g' \ -e 's+%%CFLAGS%%+${CFLAGS} -I${LOCALBASE}/include+g' \ -e 's+%%LDFLAGS%%+${LDFLAGS}+g' \ -e 's+%%BLAS%%+${BLASLIB}+g' \ -e 's+%%LAPACK%%+${LAPACKLIB}+g' \ ${WRKSRC}/Makefile.demo post-install: @${MKDIR} ${STAGEDIR}${DOCSDIR} @(cd ${WRKSRC}/ && ${INSTALL_DATA} ${PORTDOCS} ${STAGEDIR}${DOCSDIR}) @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} @(cd ${WRKSRC}/ && ${INSTALL_DATA} ${PORTEXAMPLES} ${STAGEDIR}${EXAMPLESDIR}) test check: install @( cd ${WRKSRC} ; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} Makefile.demo \ ${_MAKE_JOBS} ${MAKE_ARGS} ${ALL_TARGET} ) ${WRKSRC}/lmdemo .include Index: head/math/linbox/Makefile =================================================================== --- head/math/linbox/Makefile (revision 534189) +++ head/math/linbox/Makefile (revision 534190) @@ -1,74 +1,75 @@ # Created by: thierry@pompo.net # $FreeBSD$ PORTNAME= linbox PORTVERSION= 1.6.3 +PORTREVISION= 1 DISTVERSIONPREFIX= v CATEGORIES= math MAINTAINER= thierry@FreeBSD.org COMMENT= C++ library for exact, high-performance linear algebra LICENSE= GPLv2 LGPL21 LICENSE_COMB= dual BUILD_DEPENDS= fflas-ffpack-config:math/fflas-ffpack LIB_DEPENDS= libgmp.so:math/gmp \ libgivaro.so:math/givaro RUN_DEPENDS= bash:shells/bash USE_GITHUB= yes GH_ACCOUNT= linbox-team USES= autoreconf blaslapack:openblas compiler:c++11-lang gmake libtool localbase pkgconfig shebangfix SHEBANG_FILES= benchmarks/perfpublisher.sh examples/test.sh \ linbox-auto-install.sh linbox-config.in tests/jenkins-maker.sh \ tests/perfpublisher.sh tests/test_leak.sh OPTIONS_DEFINE= DOXYGEN OPTIONS_RADIO= SIZE OPTIONS_RADIO_SIZE= FULL MIN OPTIONS_DEFAULT= FULL OPTIONS_SUB= yes MIN_DESC= Lightweight package, with less dependencies MIN_CONFIGURE_ON= --without-saclib FULL_DESC= Complete package with all its dependencies FULL_BUILD_DEPENDS= gnuplot:math/gnuplot FULL_LIB_DEPENDS= libflint.so:math/flint2 \ libfplll.so:math/fplll \ libiml.so:math/iml \ libm4ri.so:math/m4ri \ libm4rie.so:math/m4rie \ libmpfr.so:math/mpfr \ libntl.so:math/ntl \ libtinyxml2.so:textproc/tinyxml2 FULL_RUN_DEPENDS= gnuplot:math/gnuplot FULL_USES= ghostscript FULL_CONFIGURE_WITH= flint fplll ghostscript gnuplot iml m4ri m4rie mpfr ntl DOXYGEN_VARS= BINARY_ALIAS=sed=${LOCALBASE}/bin/gsed DOXYGEN_CONFIGURE_ENABLE=doc DOXYGEN_CONFIGURE_WITH= docdir=${DOCSDIR} DOXYGEN_BUILD_DEPENDS= gsed:textproc/gsed \ dot:graphics/graphviz \ doxygen:devel/doxygen GNU_CONFIGURE= yes # ATM expat and drivers are broken CONFIGURE_ARGS= --without-expat USE_LDCONFIG= yes TEST_TARGET= check .if defined(PACKAGE_BUILDING) CONFIGURE_ARGS+=--disable-sse --disable-sse2 --disable-sse3 --disable-ssse3 \ --disable-sse41 --disable-sse42 --disable-fma --disable-fma4 \ --disable-avx --disable-avx2 .endif pre-configure: ${REINPLACE_CMD} -e 's|@LINBOXSAGE_LIBS@||' ${WRKSRC}/linbox.pc.in .include Index: head/math/octave/Makefile =================================================================== --- head/math/octave/Makefile (revision 534189) +++ head/math/octave/Makefile (revision 534190) @@ -1,128 +1,128 @@ # Created by: chuckr@FreeBSD.org # $FreeBSD$ PORTNAME= octave PORTVERSION= ${OCTAVE_VERSION} -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= math MASTER_SITES= GNU MAINTAINER= stephen@FreeBSD.org COMMENT= High-level interactive language for numerical computations LICENSE= GPLv3 BUILD_DEPENDS= gnuplot:math/gnuplot \ ${LOCALBASE}/bin/gperf:devel/gperf \ gsed:textproc/gsed \ ${LOCALBASE}/bin/makeinfo:print/texinfo RUN_DEPENDS= gnuplot:math/gnuplot \ gsed:textproc/gsed \ ${LOCALBASE}/bin/makeinfo:print/texinfo LIB_DEPENDS= libGraphicsMagick.so:graphics/GraphicsMagick \ libarpack.so:math/arpack-ng \ libcurl.so:ftp/curl \ libfftw3.so:math/fftw3 \ libfftw3f.so:math/fftw3-float \ libfltk.so:x11-toolkits/fltk \ libftgl.so:graphics/ftgl \ libhdf5.so:science/hdf5 \ libpcre.so:devel/pcre \ libqhull.so.5:math/qhull5 \ libqrupdate.so:math/qrupdate \ libumfpack.so:math/suitesparse \ libglpk.so:math/glpk \ libgl2ps.so:print/gl2ps \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libdrm.so:graphics/libdrm \ libOSMesa.so:graphics/libosmesa \ libsundials_arkode.so:math/sundials \ libportaudio.so:audio/portaudio # libsndfile.so:audio/libsndfile # Commented out until this port no longer has vulnerabilities. USES= charsetfix fortran gmake libtool perl5 pkgconfig readline \ tar:xz compiler:c++14-lang \ desktop-file-utils gl iconv xorg USE_LDCONFIG= ${PREFIX}/lib/${PORTNAME}/${PORTVERSION} USE_PERL5= build GNU_CONFIGURE= yes USE_QT= core gui help network opengl \ qmake_build buildtools_build linguist_build \ printsupport sql widgets \ xml USE_XORG= x11 xext xfixes xft \ xcursor xinerama xrender USE_GL= gl glu OCTAVE_VERSION= ${PORTVERSION} GNU_HOST= ${ARCH}-portbld-freebsd${OSREL} PLIST_SUB= OCTAVE_VERSION=${OCTAVE_VERSION} GNU_HOST=${GNU_HOST} CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib -L${LOCALBASE}/lib/qt5 CONFIGURE_ENV= GPERF="${LOCALBASE}/bin/gperf" \ JAVA_HOME=${JAVA_HOME} \ MAKEINFO=${LOCALBASE}/bin/makeinfo \ MKINFO=${LOCALBASE}/bin/makeinfo \ MOC_QTVER=${LOCALBASE}/bin/moc \ UIC_QTVER=${LOCALBASE}/bin/uic \ RCC_QTVER=${LOCALBASE}/bin/rcc \ ac_cv_type_max_align_t=yes \ ac_cv_path_SED=${LOCALBASE}/bin/gsed CONFIGURE_ARGS= --host=${GNU_HOST} \ --with-blas="-L${LOCALBASE}/lib ${BLASLIB}" \ --with-lapack="${LAPACKLIB}" \ --enable-shared \ --disable-jit \ --disable-openmp \ --with-osmesa INFO= octave liboctave INSTALL_TARGET= install-strip OPTIONS_DEFINE= DOCS JAVA QT5 OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= OPENBLAS NETLIB ATLAS OPTIONS_DEFAULT= JAVA OPENBLAS QT5 OPTIONS_SUB= yes DOCS_CONFIGURE_ENABLE= docs JAVA_CONFIGURE_ENABLE= java QT5_CONFIGURE_WITH= qt=5 qscintilla QT5_LIB_DEPENDS= libqscintilla2_qt5.so:devel/qscintilla2-qt5 DOCS_USE= TEX=dvipsk:build,formats:build JAVA_USE= JAVA=yes QT5_USES= qt:5 OPENBLAS_USES= blaslapack:openblas NETLIB_USES= blaslapack:netlib ATLAS_USES= blaslapack:atlas post-patch: ${REINPLACE_CMD} 's+"makeinfo"+"${LOCALBASE}/bin/makeinfo"+' ${WRKSRC}/libinterp/corefcn/help.cc ${REINPLACE_CMD} 's/"-qt$$qt_version"/"-qt=qt$$qt_version"/' ${WRKSRC}/configure post-install: (cd ${STAGEDIR}${DATADIR} && ${LN} -s ${PORTVERSION}/imagelib .) post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} .for file in liboctave/liboctave.ps \ refcard/refcard-a4.ps refcard/refcard-legal.ps \ refcard/refcard-letter.ps interpreter/octave.ps ${INSTALL_DATA} ${WRKSRC}/doc/${file} ${STAGEDIR}${DOCSDIR} .endfor @${MKDIR} ${STAGEDIR}${PREFIX}/${INFO_PATH} .for file in interpreter/octave.info liboctave/liboctave.info ${INSTALL_DATA} ${WRKSRC}/doc/${file} ${STAGEDIR}${PREFIX}/${INFO_PATH} .endfor check regression-test: build @(cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} check) .include "Makefile.version" .include Index: head/math/openturns/Makefile =================================================================== --- head/math/openturns/Makefile (revision 534189) +++ head/math/openturns/Makefile (revision 534190) @@ -1,52 +1,52 @@ # $FreeBSD$ PORTNAME= openturns DISTVERSIONPREFIX= v DISTVERSION= 1.14 -PORTREVISION= 4 +PORTREVISION= 5 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 LIB_DEPENDS= libceres.so:math/ceres-solver \ libcminpack.so:math/cminpack \ libgflags.so:devel/gflags \ libglog.so:devel/glog \ libnlopt.so:math/nlopt \ libopt.so:math/optpp \ libtbb.so:devel/tbb \ libhmat-oss.so:math/hmat-oss USES= bison blaslapack:openblas cmake compiler:c++11-lang eigen:3 gnome localbase:ldflags pkgconfig USE_GITHUB= yes USE_GNOME= libxml2 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 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/swig3.0 PYTHON_BUILD_DEPENDS= swig3.0:devel/swig30 \ ${PYTHON_RUN_DEPENDS} PYTHON_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} PORTEXAMPLES= * post-install: @${RM} -r ${STAGEDIR}${DOCSDIR} .include Index: head/math/primme/Makefile =================================================================== --- head/math/primme/Makefile (revision 534189) +++ head/math/primme/Makefile (revision 534190) @@ -1,58 +1,59 @@ # $FreeBSD$ PORTNAME= primme DISTVERSIONPREFIX= v DISTVERSION= 3.1 +PORTREVISION= 1 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Iterative eigensolver for symmetric and hermitian matrices LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING.txt TEST_DEPENDS= gfortran${GCC_DEFAULT}:lang/gcc${GCC_DEFAULT} USES= gmake localbase:ldflags USE_GITHUB= yes MAKEFILE= makefile ALL_TARGET= solib USE_LDCONFIG= yes BINARY_ALIAS= make=${GMAKE} CFLAGS+= -fPIC LDFLAGS+= ${LAPACKLIB} -lm OPTIONS_RADIO= LINALG OPTIONS_RADIO_LINALG= ATLAS GOTOBLAS NETLIB OPENBLAS OPTIONS_DEFAULT= OPENBLAS LINALG_DESC= Choose which linear algebra interface (LAPACK) implementation to use: GOTOBLAS_DESC= Goto blas implementation ATLAS_USES= blaslapack:atlas GOTOBLAS_USES= blaslapack:gotoblas NETLIB_USES= blaslapack:netlib NETLIB_LDFLAGS= -lblas # XXX why this isn't covered by blaslapack:netlib? OPENBLAS_USES= blaslapack:openblas TEST_ENV= ${MAKE_ENV} LDFLAGS="-lm -Wl,-rpath=${LOCALBASE}/lib/gcc${GCC_DEFAULT} ${LOCALBASE}/lib/gcc${GCC_DEFAULT}/libgcc_s.so" \ USE_MPI=no USE_PETSC=no PETSC_DIR=${LOCALBASE} TEST_ARGS= F77=gfortran${GCC_DEFAULT} FC=gfortran${GCC_DEFAULT} FLDR=gfortran${GCC_DEFAULT} TEST_TARGET= all_tests test PLIST_FILES= include/primme.h \ include/primme_eigs.h \ include/primme_eigs_f77.h \ include/primme_eigs_f90.inc \ include/primme_f77.h \ include/primme_f90.inc \ include/primme_svds.h \ include/primme_svds_f77.h \ include/primme_svds_f90.inc \ lib/libprimme.so \ lib/libprimme.so.3 \ lib/libprimme.so.3.0 .include Index: head/math/py-numpy/Makefile =================================================================== --- head/math/py-numpy/Makefile (revision 534189) +++ head/math/py-numpy/Makefile (revision 534190) @@ -1,78 +1,78 @@ # Created by: Tony Maher # $FreeBSD$ PORTNAME= numpy PORTVERSION= 1.16.5 -PORTREVISION= 4 +PORTREVISION= 5 PORTEPOCH= 1 CATEGORIES= math python MASTER_SITES= CHEESESHOP \ https://docs.scipy.org/doc/${PORTNAME}-${PORTVERSION}/:doc PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTFILES= ${DISTNAME}${EXTRACT_SUFX} \ ${PORTNAME}-ref-${PORTVERSION:R}.1.pdf:doc \ ${PORTNAME}-user-${PORTVERSION:R}.1.pdf:doc EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= python@FreeBSD.org COMMENT= The New Numeric Extension to Python LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}pytest>=0:devel/py-pytest@${PY_FLAVOR} USES= fortran python zip USE_PYTHON= allflavors autoplist concurrent cython distutils GCCLIBDIR_CMDS= ${FC} -print-file-name=libgfortran.so | ${SED} -e s/libgfortran.so// LDFLAGS+= -shared PYDISTUTILS_BUILDARGS= --fcompiler=gnu95 PYDISTUTILS_CONFIGUREARGS= --fcompiler=gnu95 PORTDOCS= * OPTIONS_DEFINE= DOCS SUITESPARSE OPTIONS_SINGLE= BLASLIB OPTIONS_SINGLE_BLASLIB= ATLAS NETLIB OPENBLAS OPTIONS_DEFAULT= OPENBLAS SUITESPARSE SUITESPARSE_DESC= Use AMD and UMFPACK in SuiteSparse ATLAS_USES= blaslapack:atlas ATLAS_VARS= BLASLIBS="ptf77blas, ptcblas" BLASNAME=atlas LAPACKLIBS=alpack LIBRARIES=atlas_libs NETLIB_USES= blaslapack:netlib NETLIB_VARS= BLASLIBS="blas, cblas" BLASNAME=atlas LAPACKLIBS=lapack LIBRARIES=atlas_libs NETLIB_LIB_DEPENDS= libcblas.so:math/cblas OPENBLAS_USES= blaslapack:openblas OPENBLAS_VARS= BLASLIBS="openblas, gfortran" BLASNAME=openblas LAPACKLIBS="openblas, gfortran" LIBRARIES=libraries SUITESPARSE_LIB_DEPENDS=libumfpack.so:math/suitesparse post-extract: @${TOUCH} ${WRKSRC}/numpy/f2py/tests/src/temp post-patch: @${REINPLACE_CMD} -e 's|%%FC%%|${FC}|' ${WRKSRC}/numpy/distutils/fcompiler/gnu.py @${CP} ${FILESDIR}/site.cfg ${WRKSRC}/site.cfg post-patch-SUITESPARSE-off: @${REINPLACE_CMD} -e 's|:%%LOCALBASE%%/include/suitesparse||' ${WRKSRC}/site.cfg pre-configure: ${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g' \ -e 's|%%BLASLIBS%%|${BLASLIBS}|; s|%%BLASNAME%%|${BLASNAME}|' \ -e 's|%%LAPACKLIBS%%|${LAPACKLIBS}|; s|%%LIBRARIES%%|${LIBRARIES}|' \ ${WRKSRC}/site.cfg @${REINPLACE_CMD} -e "s|%%GCCLIBDIR%%|$$(${GCCLIBDIR_CMDS})|" ${WRKSRC}/site.cfg ${WRKSRC}/numpy/distutils/system_info.py post-install: ${FIND} ${STAGEDIR}${PYTHON_SITELIBDIR} -name '*.so' | ${XARGS} ${STRIP_CMD} post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${PORTNAME}-ref-${PORTVERSION:R}.1.pdf ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DISTDIR}/${PORTNAME}-user-${PORTVERSION:R}.1.pdf ${STAGEDIR}${DOCSDIR} do-test: @cd ${WRKSRC} && ${PYTHON_CMD} runtests.py .include Index: head/math/py-scs/Makefile =================================================================== --- head/math/py-scs/Makefile (revision 534189) +++ head/math/py-scs/Makefile (revision 534190) @@ -1,26 +1,26 @@ # $FreeBSD$ PORTNAME= scs DISTVERSION= 2.1.1-2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Splitting conic solver for Python LICENSE= MIT BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.13.2:science/py-scipy@${PY_FLAVOR} RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.13.2:science/py-scipy@${PY_FLAVOR} USES= python blaslapack:openblas fortran # fortran is for openblas USE_PYTHON= distutils autoplist CONFIGURE_ENV= BLAS_LAPACK_LIBS="openblas" MAKE_ENV= ${CONFIGURE_ENV} .include Index: head/math/scilab/Makefile =================================================================== --- head/math/scilab/Makefile (revision 534189) +++ head/math/scilab/Makefile (revision 534190) @@ -1,181 +1,181 @@ # Created by: js@jeannot.org # $FreeBSD$ PORTNAME= scilab PORTVERSION= 5.5.2 -PORTREVISION= 24 +PORTREVISION= 25 CATEGORIES= math cad java MASTER_SITES= https://www.scilab.org/download/${PORTVERSION}/ DISTFILES= ${DISTNAME}-src${EXTRACT_SUFX} MAINTAINER= makc@FreeBSD.org COMMENT= Scientific software package for numerical computations LICENSE= GPLv2 BSD3CLAUSE LICENSE_COMB= dual LICENSE_FILE_GPLv2= ${WRKSRC}/COPYING LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/COPYING-BSD # A partial dependencies list can be found at: # http://wiki.scilab.org/Dependencies_of_Scilab_5.X LIB_DEPENDS= libxml2.so:textproc/libxml2 \ libpcre.so:devel/pcre \ libcurl.so:ftp/curl \ libhdf5.so:science/hdf5 \ libarpack.so:math/arpack-ng \ libfftw3.so:math/fftw3 \ libmatio.so:math/matio \ libamd.so:math/suitesparse RUN_DEPENDS= xdg-open:devel/xdg-utils USES= cpe desktop-file-utils fortran gettext gmake gnome iconv \ libtool ncurses pathfix pkgconfig shared-mime-info USE_CXXSTD= gnu++98 USE_LOCALE= en_US.UTF-8 GNU_CONFIGURE= yes INSTALLS_ICONS= yes CPPFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib CONFIGURE_ARGS= --with-gfortran \ --without-emf \ -disable-static-system-lib CONFIGURE_ENV= BLAS_LIBS="${BLASLIB}" LAPACK_LIBS="${LAPACKLIB}" INSTALL_TARGET= install-strip TEST_TARGET= check # XXX: tests fail MAKE_JOBS_UNSAFE= yes PLIST_SUB= SHLIB_VER=${PORTVERSION} OPTIONS_DEFINE= GUI OCAML TK OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= ATLAS NETLIB OPENBLAS OPTIONS_DEFAULT= GUI NETLIB OCAML TK OPTIONS_SUB= yes ATLAS_USES= blaslapack:atlas NETLIB_USES= blaslapack:netlib OPENBLAS_USES= blaslapack:openblas GUI_DESC= Java-based Graphical User Interface OCAML_DESC= Scicos - dynamical system simulator (requires GUI) # Java dependencies: _GUI_DEPENDS+= ${JAVALIBDIR}/flexdock.jar:devel/flexdock \ ${JAVALIBDIR}/jogl2.jar:graphics/jogamp-jogl \ foprep:math/jeuclid \ ${JAVALIBDIR}/jhall.jar:java/javahelp \ ${JAVALIBDIR}/jrosetta-api.jar:java/jrosetta \ ${JAVALIBDIR}/commons-logging.jar:java/apache-commons-logging \ ${JAVALIBDIR}/jgraphx.jar:java/jgraphx \ ${JAVALIBDIR}/jlatexmath.jar:math/jlatexmath \ ${LOCALBASE}/share/java/ecj-4.5.jar:lang/gcc-ecj45 # Documentation, graphic export: _GUI_DEPENDS+= ${LOCALBASE}/share/java/fop/build/fop.jar:textproc/fop \ ${JAVALIBDIR}/jlatexmath-fop.jar:math/jlatexmath \ ${LOCALBASE}/share/java/batik/lib/batik-all.jar:graphics/batik \ ${JAVALIBDIR}/avalon-framework.jar:devel/avalon-framework \ ${JAVALIBDIR}/commons-io.jar:devel/apache-commons-io \ ${JAVALIBDIR}/xmlgraphics-commons.jar:graphics/xmlgraphics-commons # Code quality: _GUI_DEPENDS+= ${JAVALIBDIR}/commons-beanutils.jar:java/apache-commons-beanutils \ ${JAVALIBDIR}/antlr.jar:devel/antlr \ ${JAVALIBDIR}/junit4.jar:java/junit \ ${LOCALBASE}/bin/splint:devel/splint # Documentation building: _GUI_DEPENDS+= ${LOCALBASE}/share/xsl/docbook/javahelp/javahelp.xsl:textproc/docbook-xsl \ ${JAVALIBDIR}/saxon9he.jar:textproc/saxon-he \ ${JAVALIBDIR}/xml-apis-ext.jar:textproc/xml-commons \ xsltproc:textproc/libxslt # Other gui deps: _GUI_DEPENDS+= ${JAVALIBDIR}/looks.jar:devel/looks \ ${JAVALIBDIR}/skinlf.jar:x11-toolkits/skinlf # Can't use USE_ANT because it overrides do-build target GUI_BUILD_DEPENDS= ${_GUI_DEPENDS} \ ant:devel/apache-ant GUI_RUN_DEPENDS= ${_GUI_DEPENDS} GUI_ALL_TARGET= all doc GUI_USES= gl GUI_USE= GL=gl JAVA=yes GUI_EXTRA_PATCHES= ${PATCHDIR}/extra-patch-bin-JAVA_HOME GUI_CONFIGURE_ON= --with-jdk=${JAVA_HOME} \ --with-docbook=${LOCALBASE}/share/xsl/docbook \ --enable-build-help GUI_CONFIGURE_OFF= --without-gui \ --without-javasci \ --without-xcos \ --disable-build-help OCAML_IMPLIES= GUI OCAML_CONFIGURE_WITH= modelica OCAML_BUILD_DEPENDS= ocaml:lang/ocaml OCAML_RUN_DEPENDS= ocaml:lang/ocaml TK_CONFIGURE_OFF= --without-tk TK_CONFIGURE_ON= --with-tk-library=${LOCALBASE}/lib \ --with-tk-include=${TK_INCLUDEDIR} \ --with-tcl-library=${LOCALBASE}/lib \ --with-tcl-include=${TCL_INCLUDEDIR} TK_USES= tk xorg TK_USE= XORG=x11 TK_RUN_DEPENDS= ${LOCALBASE}/lib/bwidget/init.tcl:x11-toolkits/bwidget .if !exists(/usr/include/omp.h) CONFIGURE_ARGS+= --without-openmp .endif .include .if ${PORT_OPTIONS:MGUI} && ${JAVA_PORT_VERSION:M*8*} EXTRA_PATCHES+= ${PATCHDIR}/extra-patch-Makefile.in .endif post-patch: @# Configure fixes @${REINPLACE_CMD} -e 's|-ldl | |' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|-lumfpack|-lumfpack -lsuitesparseconfig -lamd -lcholmod -lcolamd $$LAPACK_LIBS $$BLAS_LIBS|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|TCLTK_LIBS=" -ldl"|TCLTK_LIBS=" "|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|"x=" ==|"x" =|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|"x" ==|"x" =|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|sparc64-\*-netbsd\*|amd64-\*-freebsd\*|' ${WRKSRC}/configure @# Build fixes @${REINPLACE_CMD} -e 's|$$(CFLAGS:-O%=)|-I${LOCALBASE}/include -L${LOCALBASE}/lib|' ${WRKSRC}/modules/elementary_functions/Makefile.in @${REINPLACE_CMD} -e 's|freebsd|__FreeBSD__|g' ${WRKSRC}/modules/sparse/includes/spConfig.h @# malloc.h -> stdlib.h conversions @${GREP} -lr "" ${WRKSRC} \ | ${XARGS} ${REINPLACE_CMD} -e \ 's/[<"]malloc.h[>"]//' @# Run fixes @${REINPLACE_CMD} -e 's|%%JAVALIBDIR%%|${JAVALIBDIR}|' ${WRKSRC}/etc/librarypath.xml @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|' ${WRKSRC}/etc/librarypath.xml @${REINPLACE_CMD} -e 's, gfortran, ${FC},' ${WRKSRC}/modules/dynamic_link/src/scripts/configure post-patch-GUI-on: @# Configure fixes @${REINPLACE_CMD} -e 's|/usr/lib/java|${JAVALIBDIR}|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|/usr/lib64/jni|${LOCALBASE}/lib/|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|$$jardir/batik-all.jar|${LOCALBASE}/share/java/batik/lib/batik-all.jar|g' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|$$jardir/fop.jar|${LOCALBASE}/share/java/fop/build/fop.jar|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|$$jardir/jeuclid-core*.jar|${LOCALBASE}/share/java/jeuclid/repo/jeuclid-core*.jar|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|jrosetta-API.jar|jrosetta-api.jar|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|javax.media.opengl.glu.GLUnurbs|com.jogamp.opengl.glu.GLUnurbs|' ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|jogamp.common.os.MachineDescriptionRuntime|jogamp.common.os.MachineDataInfoRuntime|' ${WRKSRC}/configure @# Run fixes @${REINPLACE_CMD} -e 's|%%JAVA_HOME%%|${JAVA_HOME}|' ${WRKSRC}/bin/scilab @${REINPLACE_CMD} -e 's|/usr/share/scilab|${DATADIR}|' ${WRKSRC}/desktop/scilab.desktop @${REINPLACE_CMD} -e 's|/usr/share/scilab-cli|${DATADIR}|' \ ${WRKSRC}/desktop/scilab-adv-cli.desktop ${WRKSRC}/desktop/scilab-cli.desktop pre-install: ${MKDIR} ${STAGEDIR}${DATADIR}/.atoms post-install: @# Remove empty dirs in DATADIR/modules - they will be removed by the @# toolbox uninstaller otherwise if 3rd party toolboxes are used @${FIND} ${STAGEDIR}${DATADIR}/modules -type d -empty -delete .include Index: head/math/scs/Makefile =================================================================== --- head/math/scs/Makefile (revision 534189) +++ head/math/scs/Makefile (revision 534190) @@ -1,26 +1,26 @@ # $FreeBSD$ PORTNAME= scs DISTVERSION= 2.1.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= math MAINTAINER= yuri@FreeBSD.org COMMENT= Solver of convex cone problems via operator splitting LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt USES= gmake blaslapack:openblas fortran # fortran is for openblas USE_GITHUB= yes GH_ACCOUNT= cvxgrp USE_LDCONFIG= yes MAKE_ARGS= BLASLDFLAGS="-lopenblas" ALL_TARGET= out/libscsdir.so out/libscsindir.so post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so .include Index: head/math/suitesparse/Makefile =================================================================== --- head/math/suitesparse/Makefile (revision 534189) +++ head/math/suitesparse/Makefile (revision 534190) @@ -1,84 +1,85 @@ # Created by: Maho Nakata # $FreeBSD$ PORTNAME= suitesparse PORTVERSION= 5.7.2 +PORTREVISION= 1 DISTVERSIONPREFIX= v CATEGORIES= math MAINTAINER= fortran@FreeBSD.org COMMENT= SuiteSparse is a set of packages for sparse matrices calculation LICENSE= GPLv2 LGPL21 LICENSE_COMB= dual LIB_DEPENDS= libmetis.so:math/metis USE_GITHUB= yes GH_ACCOUNT= DrTimothyAldenDavis GH_PROJECT= SuiteSparse USES= cmake:insource fortran gmake localbase:ldflags USE_LDCONFIG= yes ALL_TARGET= library # skip demos INSTALL_TARGET= install # skip USES=cmake MAKE_ENV= BLAS="${BLASLIB}" LAPACK="${LAPACKLIB}" \ MY_METIS_LIB="-lmetis" \ JOBS="${MAKE_JOBS_NUMBER}" \ CMAKE_OPTIONS='${CMAKE_ARGS}' \ INSTALL="${STAGEDIR}${PREFIX}" \ INSTALL_DOC="${STAGEDIR}${DOCSDIR}" \ INSTALL_INCLUDE="${STAGEDIR}${PREFIX}/include/${PORTNAME}" CMAKE_ARGS= -DCMAKE_INSTALL_INCLUDEDIR:PATH="include/${PORTNAME}" \ -DBUILD_GRB_STATIC_LIBRARY:BOOL=ON LDFLAGS+= -L${WRKSRC}/lib # prevent linking with shared libs from the preinstalled older versions CONFLICTS_INSTALL= mongoose plinkseq # bin/mongoose OPTIONS_DEFINE= DOCS OPENMP TBB OPTIONS_RADIO= BLAS OPTIONS_RADIO_BLAS= ATLAS GOTOBLAS NETLIB OPENBLAS OPTIONS_DEFAULT= OPENBLAS OPENMP TBB ATLAS_USES= blaslapack:atlas GOTOBLAS_DESC= Goto blas implementation GOTOBLAS_USES= blaslapack:gotoblas NETLIB_USES= blaslapack:netlib OPENBLAS_USES= blaslapack:openblas OPENMP_USES= compiler:openmp OPENMP_MAKE_ENV_OFF= CFOPENMP= .if !exists(/usr/include/omp.h) # XXX ports/199603: LLVM openmp in base doesn't support aarch64, armv6, armv7 yet OPENMP_VARS= OPENMP=gcc- .endif TBB_DESC= Intel threading building blocks TBB_LIB_DEPENDS= libtbb.so:devel/tbb TBB_MAKE_ENV= TBB="-ltbb" SPQR_CONFIG="-DHAVE_TBB" .include .if ${ARCH} == i386 # See PR 230888 : Missing 64 bit atomic functions for i386 USES+= compiler:gcc-c++11-lib LDFLAGS+= -latomic .elif defined(PPC_ABI) && ${PPC_ABI} == ELFv1 USE_GCC= yes .else USES+= compiler:${OPENMP}c++11-lib .endif post-extract: ${RM} -r ${WRKSRC}/metis-* do-configure: # skip USES=cmake post-patch-OPENMP-off: @${REINPLACE_CMD} -e '/find_package.*OpenMP/d' \ ${WRKSRC}/GraphBLAS/CMakeLists.txt post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/* ${STAGEDIR}${PREFIX}/lib/*.so .include Index: head/math/sundials/Makefile =================================================================== --- head/math/sundials/Makefile (revision 534189) +++ head/math/sundials/Makefile (revision 534190) @@ -1,71 +1,71 @@ # $FreeBSD$ PORTNAME= sundials DISTVERSION= 3.1.2 -PORTREVISION= 9 +PORTREVISION= 11 CATEGORIES= math MASTER_SITES= https://computation.llnl.gov/projects/sundials/download/ MAINTAINER= yuri@FreeBSD.org COMMENT= SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake:noninja python:build # ninja doesn't support fortran USE_LDCONFIG= yes CMAKE_ARGS= -DPTHREAD_ENABLE:BOOL=ON \ -DBUILD_STATIC_LIBS:BOOL=OFF PLIST_SUB= SHL3=${DISTVERSION} SHL1=${DISTVERSION:R:R} SHLX3=1.1.2 SHLX1=1 OPTIONS_DEFINE= BLAS EXAMPLES LAPACK MPI # OPENMP detection is broken in cmake: https://gitlab.kitware.com/cmake/cmake/issues/17474 OPTIONS_DEFAULT= LAPACK OPTIONS_GROUP= VECTORS OPTIONS_GROUP_VECTORS= HYPRE PETSC VECTORS_DESC= Alternative vector libraries BLAS_DESC= Enable BLAS support HYPRE_DESC= HYPRE vectors support (also enables MPI) LAPACK_DESC= Use Lapack linear algebra (sets SUNDIALS_INDEX_TYPE=int32) PETSC_DESC= PETSc vectors support (also enables MPI) OPTIONS_SUB= yes BLAS_CMAKE_BOOL= BLAS_ENABLE BLAS_USES= blaslapack:openblas fortran BLAS_CMAKE_ON= -DFREEBSD_GCC_DIR:STRING=${LOCALBASE}/lib/gcc${GCC_DEFAULT:S/.//} # assumes that fortran:gcc is used EXAMPLES_CMAKE_BOOL= EXAMPLES_ENABLE_C EXAMPLES_ENABLE_CXX EXAMPLES_ENABLE_F77 EXAMPLES_ENABLE_F90 EXAMPLES_CMAKE_ON= -DEXAMPLES_INSTALL_PATH=${EXAMPLESDIR} HYPRE_CMAKE_BOOL= HYPRE_ENABLE HYPRE_CMAKE_ON= -DHYPRE_INCLUDE_DIR=${LOCALBASE}/include \ -DHYPRE_LIBRARY_DIR=${LOCALBASE}/lib HYPRE_LIB_DEPENDS= libHYPRE.so:science/hypre HYPRE_IMPLIES= MPI HYPRE_PREVENTS= LAPACK # error: Incompatible sunindextype for LAPACK; disable LAPACK and rebuild LAPACK_USES= blaslapack:openblas fortran LAPACK_CMAKE_BOOL= LAPACK_ENABLE LAPACK_CMAKE_ON= -DSUNDIALS_INDEX_TYPE:STRING=int32_t \ -DFREEBSD_GCC_DIR:STRING=${LOCALBASE}/lib/gcc${GCC_DEFAULT:S/.//} # assumes that fortran:gcc is used MPI_CMAKE_ON= -DMPI_ENABLE:BOOL=ON MPI_LIB_DEPENDS= libmpich.so:net/mpich PETSC_CMAKE_BOOL= PETSC_ENABLE PETSC_CMAKE_ON= -DPETSC_INCLUDE_DIR=${LOCALBASE}/include \ -DPETSC_LIBRARY_DIR=${LOCALBASE}/lib PETSC_LIB_DEPENDS= libpetsc.so:science/PETSc PETSC_IMPLIES= MPI PETSC_PREVENTS= LAPACK # error: Incompatible sunindextype for LAPACK; disable LAPACK and rebuild PORTEXAMPLES= * post-patch: @${FIND} ${WRKSRC}/examples -name "*.c" -o -name "*.cpp" | ${XARGS} ${REINPLACE_CMD} -E 's/"(ESYM|FSYM)"/" \1 "/g' post-install: @${RM} ${STAGEDIR}${PREFIX}/include/sundials/LICENSE .include Index: head/math/superlu/Makefile =================================================================== --- head/math/superlu/Makefile (revision 534189) +++ head/math/superlu/Makefile (revision 534190) @@ -1,71 +1,71 @@ # Created by: Pedro Giffuni # $FreeBSD$ PORTNAME= superlu PORTVERSION= 5.2.1 -PORTREVISION= 10 +PORTREVISION= 11 CATEGORIES= math MASTER_SITES= http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ \ http://crd-legacy.lbl.gov/~xiaoye/:doc DISTNAME= ${PORTNAME}_${PORTVERSION} DIST_SUBDIR= ${PORTNAME} MAINTAINER= robert.ayrapetyan@gmail.com COMMENT= Library of routines for performing sparse factorization LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/License.txt USES= cmake fortran USE_LDCONFIG= yes WRKSRC= ${WRKDIR}/SuperLU_${PORTVERSION} PLIST_SUB= P_VERSION="${PORTVERSION}" P_VER="${PORTVERSION:R:R}" CMAKE_ON= USE_XSDK_DEFAULTS CMAKE_OFF= enable_tests enable_examples PORTDOCS= * OPTIONS_DEFINE= DOCS OPTIONS_SINGLE= BLAS OPTIONS_SINGLE_BLAS= ATLAS GOTOBLAS OPENBLAS REFERENCE OPTIONS_DEFAULT= REFERENCE ATLAS_USES= blaslapack:atlas ATLAS_CMAKE_ON= -DBLA_VENDOR:STRING="ATLAS" DOCS_DISTFILES= ${DISTNAME}${EXTRACT_SUFX} \ ${SLU_DOCS:S/$/:doc/} DOCS_EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} GOTOBLAS_DESC= GotoBLAS blas implementation GOTOBLAS_USES= blaslapack:gotoblas GOTOBLAS_CMAKE_ON= -DBLA_VENDOR:STRING="Goto" OPENBLAS_DESC= OpenBLAS blas implementation OPENBLAS_USES= blaslapack:openblas OPENBLAS_CMAKE_ON= -DBLA_VENDOR:STRING="OpenBLAS" REFERENCE_DESC= Reference blas implementation REFERENCE_USES= blaslapack REFERENCE_CMAKE_ON= -DBLA_VENDOR:STRING="Generic" SLU_DOCS= SLU_general.ps.gz simax-29176.pdf post-patch: @${REINPLACE_CMD} -e \ '/CMAKE_C_FLAGS_RELEASE/s|^|#|' ${WRKSRC}/CMakeLists.txt @${REINPLACE_CMD} -e \ '/FFLAGS/s|FATAL_ERROR|WARNING|' ${WRKSRC}/cmake/XSDKDefaults.cmake post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} (cd ${DISTDIR}/${DIST_SUBDIR} && ${INSTALL_DATA} ${SLU_DOCS} \ ${STAGEDIR}${DOCSDIR}) (cd ${WRKSRC}/DOC && ${COPYTREE_SHARE} "html ug.pdf" \ ${STAGEDIR}${DOCSDIR}) do-test: @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -Denable_tests:BOOL=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include Index: head/science/berkeleygw/Makefile =================================================================== --- head/science/berkeleygw/Makefile (revision 534189) +++ head/science/berkeleygw/Makefile (revision 534190) @@ -1,36 +1,36 @@ # $FreeBSD$ PORTNAME= BerkeleyGW DISTVERSION= 2.0.0 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= https://berkeley.box.com/shared/static/ DISTFILES= wkqu37wu77tll53r8t1soe6ozqja67yy.gz MAINTAINER= yuri@FreeBSD.org COMMENT= Scientific program aimed at the ab initio virtual experimentation LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt LIB_DEPENDS= libfftw3.so:math/fftw3 USES= blaslapack:openblas gmake fortran python shebangfix SHEBANG_GLOB= *.sh *.py *awk WRKSRC= ${WRKDIR}/BGW-${DISTVERSION} BINARY_ALIAS= make=${GMAKE} gcc=${CC} MAKE_ARGS= FREEBSD_GCC_DEFAULT=${GCC_DEFAULT} FREEBSD_PREFIX=${PREFIX} INSTDIR=${STAGEDIR}${PREFIX} OPTIONS_DEFINE= DOCS EXAMPLES EXAMPLES_MAKE_ARGS= INSTALL_EXAMPLES=yes PORTEXAMPLES= * post-patch: @${LN} -s ${WRKSRC}/config/generic.serial.freebsd.mk ${WRKSRC}/arch.mk @${LN} -s ${WRKSRC}/flavor_real.mk ${WRKSRC}/flavor.mk @${FIND} ${WRKSRC} -name "script*" -o -name "*.scr" | ${XARGS} ${REINPLACE_CMD} -i '' 's|#! */bin/bash.*|#!/bin/sh|' .include Index: head/science/chemps2/Makefile =================================================================== --- head/science/chemps2/Makefile (revision 534189) +++ head/science/chemps2/Makefile (revision 534190) @@ -1,29 +1,29 @@ # $FreeBSD$ PORTNAME= CheMPS2 DISTVERSIONPREFIX= v DISTVERSION= 1.8.9 -PORTREVISION= 5 +PORTREVISION= 6 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 USES= blaslapack:openblas cmake fortran USE_GITHUB= yes GH_ACCOUNT= SebWouters USE_LDCONFIG= yes 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 Index: head/science/dlib-cpp/Makefile =================================================================== --- head/science/dlib-cpp/Makefile (revision 534189) +++ head/science/dlib-cpp/Makefile (revision 534190) @@ -1,52 +1,53 @@ # $FreeBSD$ PORTNAME= dlib DISTVERSION= 19.19 +PORTREVISION= 1 CATEGORIES= science devel math MASTER_SITES= http://dlib.net/files/ PKGNAMESUFFIX= -cpp MAINTAINER= arrowd@FreeBSD.org COMMENT= Machine learning framework written in C++ LICENSE= BSL LICENSE_FILE= ${WRKSRC}/dlib/LICENSE.txt USES= cmake compiler:c++11-lang pkgconfig tar:bzip2 USE_LDCONFIG= yes OPTIONS_DEFINE= X11 JPEG PNG GIF SQLITE BLASLAPACK PYTHON AVX OPTIONS_DEFAULT= X11 JPEG PNG GIF SQLITE BLASLAPACK_DESC= Use Blas and Lapack libraries from ports AVX_DESC= Use AVX instructions if supported by CPU X11_USES= xorg X11_USE= xorg=x11 X11_CMAKE_OFF= -DDLIB_NO_GUI_SUPPORT=1 JPEG_USES= jpeg JPEG_CMAKE_BOOL= DLIB_JPEG_SUPPORT PNG_LIB_DEPENDS= libpng.so:graphics/png PNG_CMAKE_BOOL= DLIB_PNG_SUPPORT GIF_LIB_DEPENDS= libgif.so:graphics/giflib GIF_CMAKE_BOOL= DLIB_GIF_SUPPORT SQLITE_USES= sqlite SQLITE_CMAKE_BOOL= DLIB_LINK_WITH_SQLITE3 # uses gcc until https://reviews.freebsd.org/D11482 lands BLASLAPACK_USE= gcc=yes BLASLAPACK_USES= blaslapack:openblas fortran BLASLAPACK_CMAKE_OFF= -DDLIB_USE_BLAS=0 -DDLIB_USE_LAPACK=0 -DDLIB_USE_MKL_FFT=0 # for PYTHON_PKGNAMEPREFIX PYTHON_USES= python PYTHON_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}dlib>=0:science/py-dlib@${PY_FLAVOR} PYTHON_NO_DEPENDS= yes AVX_CMAKE_BOOL= USE_AVX_INSTRUCTIONS .include Index: head/science/erkale/Makefile =================================================================== --- head/science/erkale/Makefile (revision 534189) +++ head/science/erkale/Makefile (revision 534190) @@ -1,70 +1,70 @@ # $FreeBSD$ PORTNAME= erkale DISTVERSION= g20200426 -PORTREVISION= 1 +PORTREVISION= 2 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 \ libxc.so:science/libxc RUN_DEPENDS= ${LOCALBASE}/share/erkale/basis/6-21G.gbs:science/erkale-pseudopotentials FLAVORS= serial parallel FLAVOR?= ${FLAVORS:[1]} serial_PKGNAMESUFFIX= -serial USES= cmake:noninja compiler:c11 fortran pkgconfig USE_GITHUB= yes GH_ACCOUNT= susilehtola GH_TAGNAME= 870e772f09631b3dbdd99a18e4f3d4786d684a01 USE_LDCONFIG= yes TEST_TARGET= test CMAKE_ON= BUILD_SHARED_LIBS CMAKE_ARGS= -DERKALE_SYSTEM_LIBRARY=${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 OPENBLAS_LIB_DEPENDS= libopenblas.so:math/openblas .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 Index: head/science/iboview/Makefile =================================================================== --- head/science/iboview/Makefile (revision 534189) +++ head/science/iboview/Makefile (revision 534190) @@ -1,31 +1,31 @@ # Created by: Johannes Dieterich # $FreeBSD$ PORTNAME= iboview PORTVERSION= 20150427 -PORTREVISION= 21 +PORTREVISION= 22 CATEGORIES= science MASTER_SITES= http://www.iboview.org/bin/ DISTNAME= ibo-view.20150427 MAINTAINER= jmd@FreeBSD.org COMMENT= Program for analyzing molecular electronic structure LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= boost-libs>=0:devel/boost-libs RUN_DEPENDS= boost-libs>=0:devel/boost-libs ONLY_FOR_ARCHS= amd64 USES= blaslapack:openblas fortran gl qmake:outsource qt:5 tar:bz2 USE_GL= gl glu USE_QT= buildtools_build core gui widgets opengl script svg PLIST_FILES= bin/iboview do-install: ${INSTALL_PROGRAM} ${BUILD_WRKSRC}/iboview ${STAGEDIR}${PREFIX}/bin .include Index: head/science/lammps/Makefile =================================================================== --- head/science/lammps/Makefile (revision 534189) +++ head/science/lammps/Makefile (revision 534190) @@ -1,127 +1,128 @@ # $FreeBSD$ 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= libfftw3.so:math/fftw3 USES= blaslapack:openblas cmake:noninja compiler:c++11-lang eigen:3 fortran localbase:ldflags shebangfix USE_GITHUB= yes GH_TAGNAME= patch_5May2020 USE_LDCONFIG= yes 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}} 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_BODY PKG_CLASS2 PKG_COLLOID PKG_COMPRESS PKG_DIPOLE CMAKE_ON+= PKG_GRANULAR PKG_KSPACE PKG_MANYBODY PKG_MC PKG_MESSAGE PKG_MISC PKG_MOLECULE PKG_PERI PKG_POEMS PKG_QEQ CMAKE_ON+= PKG_REPLICA PKG_RIGID PKG_SHOCK PKG_SPIN PKG_SNAP PKG_SRD CMAKE_ON+= PKG_USER-ATC PKG_USER-AWPMD PKG_USER-BOCS PKG_USER-CGDNA PKG_USER-MESODPD PKG_USER-CGSDK PKG_USER-COLVARS CMAKE_ON+= PKG_USER-DIFFRACTION PKG_USER-DPD PKG_USER-DRUDE PKG_USER-EFF PKG_USER-FEP CMAKE_ON+= PKG_USER-MANIFOLD PKG_USER-MEAMC PKG_USER-MGPT PKG_USER-MISC PKG_USER-MOFFF PKG_USER-MOLFILE CMAKE_ON+= PKG_USER-PHONON PKG_USER-PTM PKG_USER-QTB PKG_USER-REACTION CMAKE_ON+= PKG_USER-REAXC PKG_USER-SDPD PKG_USER-SMD PKG_USER-SMTBQ PKG_USER-SPH PKG_USER-TALLY CMAKE_ON+= PKG_USER-UEF PKG_USER-QMMM PKG_USER-YAFF # Packages requiring extra downloades or dependencies: PKG_MSCG PKG_USER-ADIOS2 PKG_USER-NETCDF PKG_USER-QUIP PKG_USER-SCAFACOS OPTIONS_DEFINE= JPEG PNG GZIP FFMPEG OPTIONS_GROUP= PARALLEL PACKAGES OPTIONS_DEFAULT= 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 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 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 ${PORT_OPTIONS:MOPENMP} CMAKE_ARGS+= -DBUILD_OMP:BOOL=true .endif post-patch: @${REINPLACE_CMD} 's|SHELL = /bin/bash|SHELL = ${LOCALBASE}/bin/bash|' ${WRKSRC}/src/Makefile post-patch-FFMPEG-off: @${REINPLACE_CMD} 's|find_program(FFMPEG_EXECUTABLE|#&|' ${WRKSRC}/cmake/CMakeLists.txt post-install: @${RM} -r ${STAGEDIR}${PREFIX}/lib/python* .include Index: head/science/libcint/Makefile =================================================================== --- head/science/libcint/Makefile (revision 534189) +++ head/science/libcint/Makefile (revision 534190) @@ -1,28 +1,28 @@ # $FreeBSD$ PORTNAME= libcint DISTVERSIONPREFIX= v DISTVERSION= 3.0.19 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= General GTO integrals for quantum chemistry LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libopenblas.so:math/openblas USES= cmake blaslapack:openblas USE_GITHUB= yes GH_ACCOUNT= sunqm USE_LDCONFIG= yes PLIST_FILES= include/cint.h \ include/cint_funcs.h \ lib/libcint.so \ lib/libcint.so.${PORTVERSION:R:R} \ lib/libcint.so.${PORTVERSION} .include Index: head/science/opensim-core/Makefile =================================================================== --- head/science/opensim-core/Makefile (revision 534189) +++ head/science/opensim-core/Makefile (revision 534190) @@ -1,55 +1,56 @@ # $FreeBSD$ PORTNAME= OpenSim DISTVERSION= 4.1 +PORTREVISION= 1 CATEGORIES= science PKGNAMESUFFIX= -core MAINTAINER= yuri@FreeBSD.org COMMENT= Software for modeling of musculoskeletal structures LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt BUILD_DEPENDS= bash:shells/bash LIB_DEPENDS= libdocopt.so:devel/docopt.cpp \ libSimTKcommon.so:science/simbody USES= blaslapack:openblas cmake compiler:c++11-lib fortran gl shebangfix xorg # fortran only for simbody/openblas SHEBANG_FILES= Applications/opensim-install-command-line.sh USE_GITHUB= yes GH_ACCOUNT= ${PORTNAME:tl}-org GH_PROJECT= ${PORTNAME:tl}-core USE_GL= gl glu glut USE_XORG= xi xmu USE_LDCONFIG= yes CXXFLAGS+= -I${LOCALBASE}/include/docopt CONFIGURE_ENV+= SIMBODY_HOME=${LOCALBASE} CMAKE_OFF= OPENSIM_COPY_DEPENDENCIES DO_TESTING OPTIONS_DEFINE= PYTHON JAVA DOCS OPTIONS_DEFAULT= PYTHON JAVA OPTIONS_SUB= yes PYTHON_CMAKE_BOOL= BUILD_PYTHON_WRAPPING PYTHON_USES= python PYTHON_BUILD_DEPENDS= swig3.0:devel/swig30 JAVA_CMAKE_BOOL= BUILD_JAVA_WRAPPING JAVA_CMAKE_ON= -DJAVA_AWT_LIBRARY=${LOCALBASE}/openjdk8/jre/lib/amd64/libawt.so \ -DJAVA_JVM_LIBRARY=${LOCALBASE}/openjdk8/jre/lib/amd64/server/libjvm.so \ -DJAVA_INCLUDE_PATH=${LOCALBASE}/openjdk8/include JAVA_USE= JAVA=yes JAVA_BUILD_DEPENDS= swig3.0:devel/swig30 DOCS_CMAKE_BOOL= INSTALL_DOCS PORTDOCS= * do-test: # 4 testcases are known to fail: https://github.com/opensim-org/opensim-core/issues/2379 @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DDO_TESTING=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include Index: head/science/py-phono3py/Makefile =================================================================== --- head/science/py-phono3py/Makefile (revision 534189) +++ head/science/py-phono3py/Makefile (revision 534190) @@ -1,31 +1,31 @@ # $FreeBSD$ PORTNAME= phono3py DISTVERSION= 1.13.3.27 -PORTREVISION= 6 +PORTREVISION= 7 CATEGORIES= science python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Software to calculate phonon-phonon interaction and related properties LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}phonopy>=1.13.2:science/py-phonopy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} \ ${LOCALBASE}/include/lapacke.h:math/lapacke RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}h5py>0:science/py-h5py@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}phonopy>=1.13.2:science/py-phonopy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} USES= blaslapack:openblas localbase python USE_PYTHON= distutils cython autoplist .include Index: head/science/simbody/Makefile =================================================================== --- head/science/simbody/Makefile (revision 534189) +++ head/science/simbody/Makefile (revision 534190) @@ -1,53 +1,53 @@ # $FreeBSD$ PORTNAME= simbody DISTVERSIONPREFIX= Simbody- DISTVERSION= 3.7 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science biology PATCH_SITES= https://github.com/${PORTNAME}/${PORTNAME}/commit/ PATCHFILES= 1b306f66bcd15e9bf6b27882e2daa6375ac4cd2e.patch:-p1 MAINTAINER= yuri@FreeBSD.org COMMENT= Multibody dynamics library for (bio)mechanical systems simulation LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libopenblas.so:math/openblas USES= blaslapack:openblas cmake compiler:c++11-lang fortran # fortran only for openblas USE_GITHUB= yes USE_LDCONFIG= yes CMAKE_OFF= BUILD_TESTING CMAKE_ARGS= -DBLAS_LIBRARIES:STRING=${LOCALBASE}/lib/libopenblas.so -DLAPACK_LIBRARIES:STRING=${LOCALBASE}/lib/libopenblas.so -DFREEBSD_EXAMPLESDIR=${EXAMPLESDIR} OPTIONS_DEFINE= DOCS VISUALIZER EXAMPLE_PROGRAMS # EXAMPLE_PROGRAMS significanly increases the build time and package size, so it is not called EXAMPLES to prevent it from being installed by default OPTIONS_DEFAULT= VISUALIZER OPTIONS_SUB= yes DOCS_CMAKE_BOOL= INSTALL_DOCS VISUALIZER_DESC= Build the visualizer component VISUALIZER_CMAKE_BOOL= BUILD_VISUALIZER VISUALIZER_USES= gl xorg VISUALIZER_USE= GL=gl,glu,glut XORG=xi,xmu EXAMPLE_PROGRAMS_DESC= Build and install example programs EXAMPLE_PROGRAMS_CMAKE_BOOL= BUILD_EXAMPLES PORTDOCS= * # this port installs examples into ${EXAMPLESDIR} when EXAMPLE_PROGRAMS=ON, but check-plist doesn't complain for some reason post-install-DOCS-on: # https://github.com/simbody/simbody/issues/652 @${RMDIR} ${STAGEDIR}${DOCSDIR}/api do-test: @cd ${BUILD_WRKSRC} && \ ${SETENV} ${CONFIGURE_ENV} ${CMAKE_BIN} ${CMAKE_ARGS} -DBUILD_TESTING=ON ${CMAKE_SOURCE_PATH} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} ${ALL_TARGET} && \ ${SETENV} ${MAKE_ENV} ${MAKE_CMD} ${MAKE_ARGS} test .include