diff --git a/science/avogadro2/Makefile b/science/avogadro2/Makefile index a700ba14da24..6c27820fbef0 100644 --- a/science/avogadro2/Makefile +++ b/science/avogadro2/Makefile @@ -1,32 +1,33 @@ PORTNAME= avogadro2 DISTVERSION= 2.0.0 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Chemical editor and visualization application WWW= https://two.avogadro.cc \ https://www.openchemistry.org/projects/avogadro2 \ https://github.com/OpenChemistry/avogadroapp LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= hdf5>0:science/hdf5 LIB_DEPENDS= libAvogadroCore.so:science/avogadrolibs \ libMoleQueueClient.so:misc/molequeue RUN_DEPENDS= obabel:science/openbabel USES= cmake compiler:c++11-lang desktop-file-utils gl libarchive qt:5 USE_QT= core concurrent gui network widgets buildtools:build qmake:build USE_GL= gl glew glu USE_GITHUB= yes GH_ACCOUNT= OpenChemistry GH_PROJECT= avogadroapp GH_TUPLE= flathub:shared-modules:1bb5393:flathub_shared_modules/flatpak/shared-modules \ openchemistry:avogadro-i18n:16142cf:i18n/../avogadro-i18n post-install: @${RM} -r ${STAGEDIR}${PREFIX}/share/doc .include diff --git a/science/gchemutils/Makefile b/science/gchemutils/Makefile index 644ef599a5f7..0d4263223fd5 100644 --- a/science/gchemutils/Makefile +++ b/science/gchemutils/Makefile @@ -1,70 +1,70 @@ PORTNAME= gchemutils PORTVERSION= 0.14.17 -PORTREVISION= 5 +PORTREVISION= 6 CATEGORIES= science MASTER_SITES= SAVANNAH/${PORTNAME}/${PORTVERSION:R} DISTNAME= gnome-chemistry-utils-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= C++ classes and Gtk3 widgets related to chemistry WWW= https://www.nongnu.org/gchemutils/ LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/bodr.pc:science/bodr \ ${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:science/chemical-mime-data LIB_DEPENDS= libopenbabel.so:science/openbabel \ libgoffice-0.10.so:devel/goffice RUN_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/bodr.pc:science/bodr \ ${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:science/chemical-mime-data PORTSCOUT= limitw:1,even USES= compiler:c++11-lang desktop-file-utils gettext gl gmake gnome \ libtool:keepla localbase:ldflags pathfix pkgconfig \ shared-mime-info tar:xz xorg USE_CXXSTD= c++14 USE_XORG= x11 USE_GNOME= cairo gtk30 intlhack libgsf libxml2 USE_GL= gl USE_LDCONFIG= yes GNU_CONFIGURE= yes GNU_CONFIGURE_MANPREFIX=${PREFIX}/share CONFIGURE_ARGS= --with-omf-dir=${PREFIX}/share/omf GLIB_SCHEMAS= org.gnome.gchemutils.crystal.gschema.xml \ org.gnome.gchemutils.gschema.xml \ org.gnome.gchemutils.paint.gschema.xml \ org.gnome.gchemutils.paint.plugins.arrows.gschema.xml VER= ${PORTVERSION:R} PLIST_SUB= VER=${VER} GOFFICE=0.10 VERSION=${PORTVERSION} OPTIONS_DEFINE= GNUMERIC XUL OPTIONS_SUB= yes GNUMERIC_DESC= Build gnumeric plugin XUL_DESC= Build browser plugin (requires libxul) XUL_BROKEN= XULrunner and non-Flash plugins are no longer supported XUL_CONFIGURE_ON=--enable-mozilla-plugin \ --with-mozilla-libdir=${PREFIX}/lib/xulrunner XUL_CONFIGURE_OFF=--disable-mozilla-plugin .include .if ${PORT_OPTIONS:MGNUMERIC} || exists(${LOCALBASE}/lib/libspreadsheet.so) LIB_DEPENDS+= libspreadsheet.so:math/gnumeric PLIST_SUB+= GNUMERIC="" .else PLIST_SUB+= GNUMERIC="@comment " .endif pre-configure: ${REINPLACE_CMD} -e 's|-ldl||g' ${WRKSRC}/libs/gcp/Makefile.in ${REINPLACE_CMD} -e 's|openbabel-2.0|openbabel-3|' ${WRKSRC}/${CONFIGURE_SCRIPT} post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so.* @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*/*/*/*/*.so .include diff --git a/science/kalzium/Makefile b/science/kalzium/Makefile index 8a6ab473699a..ae8b8f5a68b2 100644 --- a/science/kalzium/Makefile +++ b/science/kalzium/Makefile @@ -1,35 +1,35 @@ PORTNAME= kalzium DISTVERSION= ${KDE_APPLICATIONS_VERSION} -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= science education kde kde-applications MAINTAINER= kde@FreeBSD.org COMMENT= Periodic table of elements for KDE WWW= https://www.kde.org/applications/education/kalzium LICENSE= GPLv2 LGPL20 GFDL LICENSE_COMB= multi BUILD_DEPENDS= ${LOCALBASE}/lib/ocaml/facile/facile.a:math/facile \ ${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:science/chemical-mime-data LIB_DEPENDS= libAvogadroCore.so:science/avogadrolibs \ libopenbabel.so:science/openbabel RUN_DEPENDS= ${LOCALBASE}/libdata/pkgconfig/chemical-mime-data.pc:science/chemical-mime-data USES= cmake compiler:c++17-lang desktop-file-utils gettext-tools gl \ kde:6 ocaml:build pkgconfig qt:6 tar:xz xorg USE_GL= opengl USE_KDE= attica colorscheme completion config configwidgets \ coreaddons crash doctools guiaddons i18n itemviews \ jobwidgets kio newstuff plotting service sonnet textwidgets \ unitconversion widgetsaddons xmlgui \ ecm:build USE_LDCONFIG= yes USE_QT= 5compat base declarative scxml svg USE_XORG= x11 PIE_UNSAFE= yes OPTIONS_DEFINE= DOCS .include diff --git a/science/libghemical/Makefile b/science/libghemical/Makefile index c23677d26399..216608f51a67 100644 --- a/science/libghemical/Makefile +++ b/science/libghemical/Makefile @@ -1,39 +1,39 @@ PORTNAME= libghemical PORTVERSION= 3.0.0 -PORTREVISION= 21 +PORTREVISION= 22 CATEGORIES= science MASTER_SITES= http://bioinformatics.org/ghemical/download/release20111012/ \ http://bioinformatics.org/ghemical/download/current/ MAINTAINER= yuri@FreeBSD.org COMMENT= Support libraries of science/ghemical port WWW= https://www.bioinformatics.org/ghemical/ghemical/index.html LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING BUILD_DEPENDS= obabel:science/openbabel \ intltool-update:textproc/intltool \ ld:devel/binutils LIB_DEPENDS= libblas.so:math/blas \ libint.so:science/libint \ libf2c.so:lang/f2c \ liblapack.so:math/lapack \ libmpqc.so:science/mpqc USES= fortran gettext gl gmake libtool localbase pathfix pkgconfig USE_CXXSTD= c++98 USE_GL= gl GNU_CONFIGURE= yes USE_LDCONFIG= yes CONFIGURE_ARGS+= --enable-mpqc LDFLAGS+= -lSCbasis -lSCcints -lSCclass -lSCcontainer -lSCdft -lSCgroup \ -lSCintv3 -lSCisosurf -lSCkeyval -lSCmbpt -lSCmbptr12 -lSCmisc \ -lSCmolecule -lSCoint3 -lSCoptimize -lSCoptions -lSCpsi \ -lSCref -lSCrender -lSCscf -lSCscmat -lSCsolvent -lSCstate \ -lSCsymmetry -lSCwfn -lgfortran -lpthread -lblas -llapack PLIST_SUB= LIBGHEMICAL_VERSION="${PORTVERSION}" INSTALL_TARGET= install-strip .include diff --git a/science/luscus/Makefile b/science/luscus/Makefile index 45960a841f19..7e8d99a22bf1 100644 --- a/science/luscus/Makefile +++ b/science/luscus/Makefile @@ -1,37 +1,37 @@ PORTNAME= luscus DISTVERSION= 0.8.6 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= SF/${PORTNAME}/ DISTNAME= ${PORTNAME}_${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Molecular editor and viewer WWW= https://sourceforge.net/projects/luscus/ LICENSE= AFL LICENSE_NAME= Academic Free License LICENSE_FILE= ${WRKSRC}/License.txt LICENSE_PERMS= auto-accept dist-mirror pkg-mirror LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 \ libgdkglext-x11-1.0.so:x11-toolkits/gtkglext RUN_DEPENDS= bash:shells/bash \ obabel:science/openbabel # see https://sourceforge.net/p/luscus/tickets/5/ USES= cmake compiler:c++11-lang gettext-runtime gl gnome pkgconfig \ shebangfix xorg SHEBANG_GLOB= *.sh USE_GNOME= atk cairo gdkpixbuf glib20 gtk20 pango pangox-compat USE_GL= gl glu USE_XORG= x11 CFLAGS+= -fcommon # variables n_geometries/move_molecule/window/pix/etc are defined in the header post-patch: @${REINPLACE_CMD} 's|/etc/luscus|${DATADIR}|' ${WRKSRC}/gv_system.c @${REINPLACE_CMD} -i '' 's|$$HOME/\.${PORTNAME}/|${LOCALBASE}/bin/|' ${WRKSRC}/*/*/*.sh @${REINPLACE_CMD} -i '' 's|$$RUNDIR/|${LOCALBASE}/bin/|' ${WRKSRC}/*/*/*.sh .include diff --git a/science/molsketch/Makefile b/science/molsketch/Makefile index c071685b4325..490fa53a817e 100644 --- a/science/molsketch/Makefile +++ b/science/molsketch/Makefile @@ -1,32 +1,33 @@ PORTNAME= molsketch DISTVERSION= 0.8.2 +PORTREVISION= 1 DISTVERSIONSUFFIX= -src CATEGORIES= science MASTER_SITES= SF/${PORTNAME}/Molsketch/ DISTNAME= Molsketch-${DISTVERSIONFULL} MAINTAINER= yuri@FreeBSD.org COMMENT= 2D molecule editor WWW= https://molsketch.sourceforge.io/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libopenbabel.so:science/openbabel USES= cmake compiler:c++20-lang desktop-file-utils gl localbase:ldflags \ pkgconfig qt:6 shared-mime-info # build fails with ninja, see https://sourceforge.net/p/molsketch/bugs/41/ USE_QT= base svg tools:build USE_LDCONFIG= ${PREFIX}/lib/molsketch USE_GL= gl opengl CMAKE_ARGS= -DMSK_PREFIX:STRING=${PREFIX} CMAKE_ON= MSK_QT6 OPTIONS_DEFINE= DOCS WRKSRC= ${WRKDIR}/Molsketch-${DISTVERSION} PORTDOCS= * .include diff --git a/science/openbabel/Makefile b/science/openbabel/Makefile index 0dc26cebd570..c9362d756734 100644 --- a/science/openbabel/Makefile +++ b/science/openbabel/Makefile @@ -1,71 +1,67 @@ PORTNAME= openbabel -DISTVERSION= 3-1-1-178 -PORTREVISION= 6 -#DISTVERSIONSUFFIX= -source -DISTVERSIONSUFFIX= -g2b211d6ac +DISTVERSIONPREFIX= ${PORTNAME}- +DISTVERSION= 3-2-0 CATEGORIES= science -#MASTER_SITES= https://github.com/openbabel/openbabel/releases/download/openbabel-${PORTVERSION:C/\./-/g}/ MAINTAINER= yuri@FreeBSD.org COMMENT= Chemical toolbox designed to speak the many languages of chemical data -WWW= https://openbabel.org/wiki/Main_Page +WWW= https://openbabel.org/ \ + https://github.com/openbabel/openbabel LICENSE= GPLv2+ BUILD_DEPENDS= rapidjson>0:devel/rapidjson LIB_DEPENDS= libmaeparser.so:science/maeparser \ libcoordgen.so:science/coordgenlibs \ libboost_thread.so:devel/boost-libs -CONFLICTS_INSTALL= babel - USES= cmake:testing compiler:c++11-lang eigen:3 gnome perl5 pkgconfig tar:bz2 USE_CXXSTD= c++11 USE_GNOME= libxml2 USE_LDCONFIG= yes -USE_GITHUB= yes # temporary +USE_GITHUB= yes USE_PERL5= build CMAKE_ON= WITH_COORDGEN WITH_JSON OPENBABEL_USE_SYSTEM_RAPIDJSON WITH_MAEPARSER CMAKE_OFF= ENABLE_TESTS PYTHON_BINDINGS CMAKE_TESTING_ON= ENABLE_TESTS -#WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} +CONFLICTS_INSTALL= babel -PLIST_SUB= VERSION=${PORTVERSION:R} +PLIST_SUB= VERSION=${PORTVERSION} OPTIONS_DEFINE= CAIRO GUI OPTIONS_DEFAULT= CAIRO GUI OPTIONS_SUB= yes CAIRO_DESC= PNG support via cairo library CAIRO_USE= GNOME=cairo GUI_CMAKE_BOOL= BUILD_GUI GUI_CMAKE_ON= -DwxWidgets_CONFIG_EXECUTABLE:STRING=${WX_CONFIG} GUI_USE= WX=3.0 .include .if ${CHOSEN_COMPILER_TYPE} == gcc CXXFLAGS+= -Wno-narrowing USE_CXXSTD= c++11 .endif pre-configure: ${REINPLACE_CMD} -e '/pkgconfig/s,$${LIB_INSTALL_DIR},libdata,' \ ${WRKSRC}/CMakeLists.txt pre-configure-CAIRO-off: ${REINPLACE_CMD} -e '/find_package(Cairo)/d' \ ${WRKSRC}/CMakeLists.txt post-install-PYTHON-on: (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) (cd ${STAGEDIR}${PREFIX} && ${PYTHON_CMD} -O ${PYTHON_LIBDIR}/compileall.py \ -d ${PREFIX} -f ${PYTHONPREFIX_SITELIBDIR:S,${PREFIX}/,,}) -# 2 tests fail, see https://github.com/openbabel/openbabel/issues/2604 +# tests as of 3.2.0: 100% tests passed, 0 tests failed out of 337 .include diff --git a/science/openbabel/distinfo b/science/openbabel/distinfo index 8164fd7c673b..0493440f3997 100644 --- a/science/openbabel/distinfo +++ b/science/openbabel/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1688103397 -SHA256 (openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.tar.gz) = 86c4922526a5b16cd08ba187413ce6b8145705bdeb1b5dbbe0c3eb4d2bf91269 -SIZE (openbabel-openbabel-3-1-1-178-g2b211d6ac_GH0.tar.gz) = 36848606 +TIMESTAMP = 1779861753 +SHA256 (openbabel-openbabel-openbabel-3-2-0_GH0.tar.gz) = 9aadf9f01b3d0ff15d49fcd28d7d76b923218d70bf10f99ea4cc466607f4c7e2 +SIZE (openbabel-openbabel-openbabel-3-2-0_GH0.tar.gz) = 37815471 diff --git a/science/openbabel/pkg-plist b/science/openbabel/pkg-plist index 5d8e38185fe6..ca78e2c9df0e 100644 --- a/science/openbabel/pkg-plist +++ b/science/openbabel/pkg-plist @@ -1,324 +1,326 @@ bin/obabel bin/obconformer bin/obdistgen bin/obenergy bin/obfit bin/obfitall bin/obgen bin/obgrep %%GUI%%bin/obgui bin/obminimize bin/obmm bin/obprobe bin/obprop bin/obrms bin/obrotamer bin/obrotate bin/obspectrophore bin/obsym bin/obtautomer bin/obthermo include/inchi/inchi_api.h include/openbabel3/LBFGS.h include/openbabel3/LBFGS/LineSearchBacktracking.h include/openbabel3/LBFGS/LineSearchBracketing.h include/openbabel3/LBFGS/LineSearchNocedalWright.h include/openbabel3/LBFGS/Param.h include/openbabel3/openbabel/alias.h include/openbabel3/openbabel/atom.h include/openbabel3/openbabel/babelconfig.h include/openbabel3/openbabel/base.h include/openbabel3/openbabel/bitvec.h include/openbabel3/openbabel/bond.h include/openbabel3/openbabel/bondtyper.h include/openbabel3/openbabel/builder.h include/openbabel3/openbabel/canon.h include/openbabel3/openbabel/chains.h include/openbabel3/openbabel/chargemodel.h include/openbabel3/openbabel/chemdrawcdx.h include/openbabel3/openbabel/conformersearch.h include/openbabel3/openbabel/data.h include/openbabel3/openbabel/data_utilities.h include/openbabel3/openbabel/depict/asciipainter.h include/openbabel3/openbabel/depict/cairopainter.h include/openbabel3/openbabel/depict/commandpainter.h include/openbabel3/openbabel/depict/depict.h include/openbabel3/openbabel/depict/painter.h include/openbabel3/openbabel/depict/svgpainter.h include/openbabel3/openbabel/descriptor.h include/openbabel3/openbabel/distgeom.h include/openbabel3/openbabel/dlhandler.h include/openbabel3/openbabel/elements.h include/openbabel3/openbabel/fingerprint.h include/openbabel3/openbabel/forcefield.h include/openbabel3/openbabel/format.h include/openbabel3/openbabel/generic.h include/openbabel3/openbabel/graphsym.h include/openbabel3/openbabel/grid.h include/openbabel3/openbabel/griddata.h include/openbabel3/openbabel/groupcontrib.h include/openbabel3/openbabel/inchiformat.h include/openbabel3/openbabel/internalcoord.h include/openbabel3/openbabel/isomorphism.h include/openbabel3/openbabel/json.h include/openbabel3/openbabel/kekulize.h include/openbabel3/openbabel/kinetics.h include/openbabel3/openbabel/lineend.h include/openbabel3/openbabel/locale.h +include/openbabel3/openbabel/macrocycle.h include/openbabel3/openbabel/math/align.h include/openbabel3/openbabel/math/erf.h include/openbabel3/openbabel/math/matrix3x3.h include/openbabel3/openbabel/math/spacegroup.h include/openbabel3/openbabel/math/transform3d.h include/openbabel3/openbabel/math/vector3.h include/openbabel3/openbabel/matrix.h include/openbabel3/openbabel/mcdlutil.h include/openbabel3/openbabel/mol.h include/openbabel3/openbabel/molchrg.h include/openbabel3/openbabel/obconversion.h include/openbabel3/openbabel/oberror.h include/openbabel3/openbabel/obfunctions.h include/openbabel3/openbabel/obiter.h include/openbabel3/openbabel/obmolecformat.h include/openbabel3/openbabel/obutil.h include/openbabel3/openbabel/op.h include/openbabel3/openbabel/optransform.h include/openbabel3/openbabel/parsmart.h include/openbabel3/openbabel/patty.h include/openbabel3/openbabel/phmodel.h include/openbabel3/openbabel/plugin.h include/openbabel3/openbabel/pointgroup.h include/openbabel3/openbabel/query.h include/openbabel3/openbabel/reaction.h include/openbabel3/openbabel/reactionfacade.h include/openbabel3/openbabel/residue.h include/openbabel3/openbabel/ring.h include/openbabel3/openbabel/rotamer.h include/openbabel3/openbabel/rotor.h include/openbabel3/openbabel/spectrophore.h include/openbabel3/openbabel/stereo/bindings.h include/openbabel3/openbabel/stereo/cistrans.h include/openbabel3/openbabel/stereo/squareplanar.h include/openbabel3/openbabel/stereo/stereo.h include/openbabel3/openbabel/stereo/tetrahedral.h include/openbabel3/openbabel/stereo/tetranonplanar.h include/openbabel3/openbabel/stereo/tetraplanar.h include/openbabel3/openbabel/tautomer.h include/openbabel3/openbabel/text.h include/openbabel3/openbabel/tokenst.h include/openbabel3/openbabel/typer.h include/openbabel3/openbabel/xml.h lib/cmake/openbabel3/OpenBabel3Config.cmake lib/cmake/openbabel3/OpenBabel3ConfigVersion.cmake lib/cmake/openbabel3/OpenBabel3_EXPORTS-%%CMAKE_BUILD_TYPE%%.cmake lib/cmake/openbabel3/OpenBabel3_EXPORTS.cmake lib/libinchi.so -lib/libinchi.so.0 -lib/libinchi.so.0.4.1 +lib/libinchi.so.1 +lib/libinchi.so.1.07.4 lib/libopenbabel.so -lib/libopenbabel.so.7 -lib/libopenbabel.so.7.0.0 +lib/libopenbabel.so.8 +lib/libopenbabel.so.8.0.0 lib/openbabel/%%VERSION%%/APIInterface.so lib/openbabel/%%VERSION%%/CSRformat.so lib/openbabel/%%VERSION%%/MCDLformat.so lib/openbabel/%%VERSION%%/MNAformat.so lib/openbabel/%%VERSION%%/PQSformat.so lib/openbabel/%%VERSION%%/abinitformat.so lib/openbabel/%%VERSION%%/acesformat.so lib/openbabel/%%VERSION%%/acrformat.so lib/openbabel/%%VERSION%%/adfformat.so lib/openbabel/%%VERSION%%/alchemyformat.so lib/openbabel/%%VERSION%%/amberformat.so lib/openbabel/%%VERSION%%/aoforceformat.so lib/openbabel/%%VERSION%%/asciiformat.so lib/openbabel/%%VERSION%%/balstformat.so lib/openbabel/%%VERSION%%/bgfformat.so lib/openbabel/%%VERSION%%/boxformat.so lib/openbabel/%%VERSION%%/cacaoformat.so lib/openbabel/%%VERSION%%/cacheformat.so lib/openbabel/%%VERSION%%/carformat.so lib/openbabel/%%VERSION%%/castepformat.so lib/openbabel/%%VERSION%%/cccformat.so lib/openbabel/%%VERSION%%/cdxmlformat.so lib/openbabel/%%VERSION%%/chem3dformat.so lib/openbabel/%%VERSION%%/chemdoodlejsonformat.so lib/openbabel/%%VERSION%%/chemdrawcdx.so lib/openbabel/%%VERSION%%/chemdrawct.so lib/openbabel/%%VERSION%%/chemicaljsonformat.so lib/openbabel/%%VERSION%%/chemkinformat.so lib/openbabel/%%VERSION%%/chemtoolformat.so lib/openbabel/%%VERSION%%/cifformat.so lib/openbabel/%%VERSION%%/cmlformat.so lib/openbabel/%%VERSION%%/cmlreactformat.so lib/openbabel/%%VERSION%%/cofformat.so lib/openbabel/%%VERSION%%/confabreport.so lib/openbabel/%%VERSION%%/copyformat.so lib/openbabel/%%VERSION%%/crkformat.so lib/openbabel/%%VERSION%%/crystal09format.so lib/openbabel/%%VERSION%%/cssrformat.so lib/openbabel/%%VERSION%%/daltonformat.so lib/openbabel/%%VERSION%%/dlpolyformat.so lib/openbabel/%%VERSION%%/dmolformat.so lib/openbabel/%%VERSION%%/exyzformat.so lib/openbabel/%%VERSION%%/fastaformat.so lib/openbabel/%%VERSION%%/fastsearchformat.so lib/openbabel/%%VERSION%%/fchkformat.so lib/openbabel/%%VERSION%%/featformat.so lib/openbabel/%%VERSION%%/fhformat.so lib/openbabel/%%VERSION%%/fhiaimsformat.so lib/openbabel/%%VERSION%%/fingerprintformat.so lib/openbabel/%%VERSION%%/fpsformat.so lib/openbabel/%%VERSION%%/freefracformat.so lib/openbabel/%%VERSION%%/gamessformat.so lib/openbabel/%%VERSION%%/gamessukformat.so lib/openbabel/%%VERSION%%/gausscubeformat.so lib/openbabel/%%VERSION%%/gaussformat.so lib/openbabel/%%VERSION%%/gausszmatformat.so lib/openbabel/%%VERSION%%/ghemicalformat.so lib/openbabel/%%VERSION%%/groformat.so lib/openbabel/%%VERSION%%/gromos96format.so lib/openbabel/%%VERSION%%/gulpformat.so lib/openbabel/%%VERSION%%/hinformat.so lib/openbabel/%%VERSION%%/inchiformat.so lib/openbabel/%%VERSION%%/jaguarformat.so +lib/openbabel/%%VERSION%%/ketformat.so lib/openbabel/%%VERSION%%/lmpdatformat.so lib/openbabel/%%VERSION%%/lpmdformat.so lib/openbabel/%%VERSION%%/maeformat.so lib/openbabel/%%VERSION%%/mdffformat.so lib/openbabel/%%VERSION%%/mdlformat.so lib/openbabel/%%VERSION%%/mmcifformat.so lib/openbabel/%%VERSION%%/mmodformat.so lib/openbabel/%%VERSION%%/mol2format.so lib/openbabel/%%VERSION%%/moldenformat.so lib/openbabel/%%VERSION%%/molproformat.so lib/openbabel/%%VERSION%%/molreport.so lib/openbabel/%%VERSION%%/mopacformat.so lib/openbabel/%%VERSION%%/mpdformat.so lib/openbabel/%%VERSION%%/mpqcformat.so lib/openbabel/%%VERSION%%/msiformat.so lib/openbabel/%%VERSION%%/msmsformat.so lib/openbabel/%%VERSION%%/nulformat.so lib/openbabel/%%VERSION%%/nwchemformat.so lib/openbabel/%%VERSION%%/opendxformat.so lib/openbabel/%%VERSION%%/orcaformat.so lib/openbabel/%%VERSION%%/outformat.so lib/openbabel/%%VERSION%%/painterformat.so lib/openbabel/%%VERSION%%/pcmodelformat.so lib/openbabel/%%VERSION%%/pdbformat.so lib/openbabel/%%VERSION%%/pdbqtformat.so lib/openbabel/%%VERSION%%/plugin_charges.so lib/openbabel/%%VERSION%%/plugin_descriptors.so lib/openbabel/%%VERSION%%/plugin_fingerprints.so lib/openbabel/%%VERSION%%/plugin_forcefields.so lib/openbabel/%%VERSION%%/plugin_ops.so %%CAIRO%%lib/openbabel/%%VERSION%%/png2format.so lib/openbabel/%%VERSION%%/pngformat.so lib/openbabel/%%VERSION%%/pointcloudformat.so lib/openbabel/%%VERSION%%/posformat.so lib/openbabel/%%VERSION%%/povrayformat.so lib/openbabel/%%VERSION%%/pqrformat.so lib/openbabel/%%VERSION%%/pubchem.so lib/openbabel/%%VERSION%%/pubchemjsonformat.so lib/openbabel/%%VERSION%%/pwscfformat.so lib/openbabel/%%VERSION%%/qchemformat.so lib/openbabel/%%VERSION%%/reportformat.so lib/openbabel/%%VERSION%%/rinchiformat.so lib/openbabel/%%VERSION%%/rsmiformat.so lib/openbabel/%%VERSION%%/rxnformat.so lib/openbabel/%%VERSION%%/shelxformat.so lib/openbabel/%%VERSION%%/siestaformat.so lib/openbabel/%%VERSION%%/smilesformat.so lib/openbabel/%%VERSION%%/smileyformat.so lib/openbabel/%%VERSION%%/stlformat.so lib/openbabel/%%VERSION%%/svgformat.so lib/openbabel/%%VERSION%%/textformat.so lib/openbabel/%%VERSION%%/thermoformat.so lib/openbabel/%%VERSION%%/tinkerformat.so lib/openbabel/%%VERSION%%/titleformat.so lib/openbabel/%%VERSION%%/turbomoleformat.so lib/openbabel/%%VERSION%%/unichemformat.so lib/openbabel/%%VERSION%%/vaspformat.so lib/openbabel/%%VERSION%%/viewmolformat.so lib/openbabel/%%VERSION%%/wlnformat.so lib/openbabel/%%VERSION%%/xedformat.so lib/openbabel/%%VERSION%%/xmlformat.so lib/openbabel/%%VERSION%%/xsfformat.so lib/openbabel/%%VERSION%%/xyzformat.so lib/openbabel/%%VERSION%%/yasaraformat.so lib/openbabel/%%VERSION%%/zindoformat.so libdata/pkgconfig/openbabel-3.pc share/man/man1/obabel.1.gz share/man/man1/obchiral.1.gz share/man/man1/obconformer.1.gz share/man/man1/obdistgen.1.gz share/man/man1/obenergy.1.gz share/man/man1/obfit.1.gz share/man/man1/obgen.1.gz share/man/man1/obgrep.1.gz share/man/man1/obgui.1.gz share/man/man1/obminimize.1.gz share/man/man1/obprobe.1.gz share/man/man1/obprop.1.gz share/man/man1/obrms.1.gz share/man/man1/obrotamer.1.gz share/man/man1/obrotate.1.gz share/man/man1/obspectrophore.1.gz share/man/man1/obsym.1.gz share/man/man1/obtautomer.1.gz share/man/man1/obthermo.1.gz share/man/man1/roundtrip.1.gz %%DATADIR%%/%%VERSION%%/MACCS.txt %%DATADIR%%/%%VERSION%%/SMARTS_InteLigand.txt %%DATADIR%%/%%VERSION%%/UFF.prm %%DATADIR%%/%%VERSION%%/atomization-energies.txt %%DATADIR%%/%%VERSION%%/atomtyp.txt %%DATADIR%%/%%VERSION%%/babel_povray3.inc %%DATADIR%%/%%VERSION%%/bondtyp.txt %%DATADIR%%/%%VERSION%%/eem.txt %%DATADIR%%/%%VERSION%%/eem2015ba.txt %%DATADIR%%/%%VERSION%%/eem2015bm.txt %%DATADIR%%/%%VERSION%%/eem2015bn.txt %%DATADIR%%/%%VERSION%%/eem2015ha.txt %%DATADIR%%/%%VERSION%%/eem2015hm.txt %%DATADIR%%/%%VERSION%%/eem2015hn.txt %%DATADIR%%/%%VERSION%%/eqeqIonizations.txt %%DATADIR%%/%%VERSION%%/gaff.dat %%DATADIR%%/%%VERSION%%/gaff.prm %%DATADIR%%/%%VERSION%%/ghemical.prm %%DATADIR%%/%%VERSION%%/logp.txt %%DATADIR%%/%%VERSION%%/mmff94.ff %%DATADIR%%/%%VERSION%%/mmff94s.ff %%DATADIR%%/%%VERSION%%/mmffang.par %%DATADIR%%/%%VERSION%%/mmffbndk.par %%DATADIR%%/%%VERSION%%/mmffbond.par %%DATADIR%%/%%VERSION%%/mmffchg.par %%DATADIR%%/%%VERSION%%/mmffdef.par %%DATADIR%%/%%VERSION%%/mmffdfsb.par %%DATADIR%%/%%VERSION%%/mmffoop.par %%DATADIR%%/%%VERSION%%/mmffpbci.par %%DATADIR%%/%%VERSION%%/mmffprop.par %%DATADIR%%/%%VERSION%%/mmffs_oop.par %%DATADIR%%/%%VERSION%%/mmffs_tor.par %%DATADIR%%/%%VERSION%%/mmffstbn.par %%DATADIR%%/%%VERSION%%/mmfftor.par %%DATADIR%%/%%VERSION%%/mmffvdw.par %%DATADIR%%/%%VERSION%%/mpC.txt %%DATADIR%%/%%VERSION%%/mr.txt %%DATADIR%%/%%VERSION%%/patterns.txt %%DATADIR%%/%%VERSION%%/phmodel.txt %%DATADIR%%/%%VERSION%%/plugindefines.txt %%DATADIR%%/%%VERSION%%/psa.txt %%DATADIR%%/%%VERSION%%/qeq.txt %%DATADIR%%/%%VERSION%%/resdata.txt %%DATADIR%%/%%VERSION%%/rigid-fragments-index.txt %%DATADIR%%/%%VERSION%%/rigid-fragments.txt %%DATADIR%%/%%VERSION%%/ring-fragments.txt %%DATADIR%%/%%VERSION%%/ringtyp.txt %%DATADIR%%/%%VERSION%%/space-groups.txt %%DATADIR%%/%%VERSION%%/splash.png %%DATADIR%%/%%VERSION%%/superatom.txt %%DATADIR%%/%%VERSION%%/svgformat.script %%DATADIR%%/%%VERSION%%/templates.sdf %%DATADIR%%/%%VERSION%%/torlib.txt %%DATADIR%%/%%VERSION%%/torsion.txt %%DATADIR%%/%%VERSION%%/types.txt diff --git a/science/v_sim/Makefile b/science/v_sim/Makefile index fa8d4d9e7fa2..78fa5b26f50e 100644 --- a/science/v_sim/Makefile +++ b/science/v_sim/Makefile @@ -1,112 +1,112 @@ PORTNAME= v_sim DISTVERSION= 3.9.1 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= science MAINTAINER= thierry@FreeBSD.org COMMENT= Visualization of atomic structures WWW= https://gitlab.com/l_sim/v_sim LICENSE= CeCILL LICENSE_NAME= CeCILL LICENSE_FILE= ${WRKSRC}/COPYING LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept BUILD_DEPENDS= p5-XML-LibXML>0:textproc/p5-XML-LibXML \ libarchive>0:archivers/libarchive \ xcrysden:science/xcrysden \ bash:shells/bash \ gtkdocize:textproc/gtk-doc LIB_DEPENDS= libgdkglext-x11-1.0.so:x11-toolkits/gtkglext \ libfontconfig.so:x11-fonts/fontconfig \ libopenbabel.so:science/openbabel \ libfreetype.so:print/freetype2 \ libepoxy.so:graphics/libepoxy \ libharfbuzz.so:print/harfbuzz \ libyaml.so:textproc/libyaml \ libnetcdf.so:science/netcdf \ libmsym.so:science/libmsym \ libpng16.so:graphics/png \ libftgl.so:graphics/ftgl \ libxc.so:science/libxc RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}numpy>=1.16:math/py-numpy@${PY_FLAVOR} \ xcrysden:science/xcrysden \ libarchive>0:archivers/libarchive \ ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} USES= autoreconf blaslapack compiler:c11 fortran gl gmake gnome \ libtool:keepla localbase:ldflags pkgconfig python \ shebangfix tar:bzip2 xorg SHEBANG_GLOB= *.py USE_XORG= x11 USE_GNOME= cairo gtk30 gdkpixbuf intltool introspection pygobject3:run USE_GL= gl glu USE_GITLAB= yes GL_ACCOUNT= l_sim GL_TAGNAME= f96c25a8aa1f4a149dd45fcb52de7216e65996a9 GNU_CONFIGURE= yes CONFIGURE_SHELL=${LOCALBASE}/bin/bash CONFIGURE_ARGS= --htmldir=${PREFIX}/share/doc --with-openbabel \ --with-netcdf=${LOCALBASE} --with-etsf-file-format \ --with-xsf --with-cube --with-msym=${LOCALBASE} \ --with-msym-inc=-I${LOCALBASE}/include/libmsym \ --with-libxc=${LOCALBASE} --enable-python-module \ --disable-gtk-doc GNU_CONFIGURE_MANPREFIX=${PREFIX}/share CPPFLAGS+= ${CFLAGS} LDFLAGS+= -lm USE_LDCONFIG= yes OPTIONS_DEFINE= DOCS NLS EXAMPLES OPTIONS_SUB= yes .if defined(WITH_DEBUG) CONFIGURE_ARGS+=--enable-debug-messages .endif .include .if ${ARCH:Mamd64*} || ${ARCH:Mpowerpc64*} BUILD_DEPENDS+= abinit:science/abinit RUN_DEPENDS+= abinit:science/abinit CONFIGURE_ARGS+=--with-abinit PLIST_SUB+= AB="" .else PLIST_SUB+= AB="@comment " .endif .if ${PORT_OPTIONS:MNLS} USES+= gettext .else USES+= gettext-tools .endif pre-configure: ${REINPLACE_CMD} -e 's|$${docdir}/examples|${EXAMPLESDIR}|' \ ${WRKSRC}/configure.ac ${REINPLACE_CMD} -e 's|print sys.prefix|print (sys.prefix)|' \ -e 's|print sys.exec_prefix|print (sys.exec_prefix)|' \ ${WRKSRC}/m4/python.m4 pre-configure-NLS-off: ${REINPLACE_CMD} -e '/^ po /d' ${WRKSRC}/Makefile.am pre-configure-DOCS-off: ${REINPLACE_CMD} -e '/^ Documentation/d' ${WRKSRC}/Makefile.am pre-configure-EXAMPLES-off: ${REINPLACE_CMD} -e '/^ examples/d' \ ${WRKSRC}/Makefile.am ${REINPLACE_CMD} -e 's|: install-v_simexamplesDATA|:|' \ ${WRKSRC}/lib/python/Makefile.am post-install: .if !defined(WITH_DEBUG) ${FIND} ${STAGEDIR}${PREFIX}/lib -type f -name "lib*.so.8.0.0" | \ ${XARGS} ${STRIP_CMD} .endif @cd ${STAGEDIR}${PREFIX} && \ ${FIND} lib/${PYTHON_VERSION} -type f -or -type l >> ${TMPPLIST} .include diff --git a/science/xcrysden/Makefile b/science/xcrysden/Makefile index e955d86e19f4..c237f4cb959a 100644 --- a/science/xcrysden/Makefile +++ b/science/xcrysden/Makefile @@ -1,54 +1,54 @@ PORTNAME= xcrysden PORTVERSION= 1.6.2 -PORTREVISION= 4 +PORTREVISION= 5 CATEGORIES= science MASTER_SITES= http://www.xcrysden.org/download/ MAINTAINER= yuri@FreeBSD.org COMMENT= Crystalline and molecular structure visualisation program WWW= http://www.xcrysden.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libfftw3.so:math/fftw3 \ libgl2ps.so:print/gl2ps \ libTogl2.0.so:graphics/togl RUN_DEPENDS= bwidget>0:x11-toolkits/bwidget \ obabel:science/openbabel \ ppmtompeg:graphics/netpbm \ xwd:x11/xwd USES= fortran gl gmake localbase:ldflags magick:run tcl tk xorg USE_GL= gl glu USE_XORG= x11 xmu CONFLICTS_INSTALL= cgnslib-4.1.2,1 # bin/unitconv MAKE_ARGS= prefix=${STAGEDIR}${PREFIX} CFLAGS+= -fcommon # notified xcrysden ML on Sep 20, 2020 BINARY_ALIAS= make=gmake gcc=cc gfortran=gfortran${GCC_DEFAULT} OPTIONS_DEFINE= EXAMPLES PORTEXAMPLES= * post-patch: @${CP} ${FILESDIR}/Make.sys ${WRKSRC} @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g' ${WRKSRC}/Make.sys @${RM} -r ${WRKSRC}/external/src post-install: # stagedir shouldn't be in executables @${REINPLACE_CMD} -i '' -e 's|${STAGEDIR}||' ${STAGEDIR}${PREFIX}/bin/* # remove bad symlinks @${RM} \ ${STAGEDIR}${PREFIX}/share/doc/xcrysden/examples/examples \ ${STAGEDIR}${PREFIX}/share/xcrysden/examples @${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/xcrysden/* # move examples from the docs dir @${MV} ${STAGEDIR}${DOCSDIR}/examples ${STAGEDIR}${EXAMPLESDIR} .include diff --git a/science/xdrawchem/Makefile b/science/xdrawchem/Makefile index 1107c82018c2..926a78490b15 100644 --- a/science/xdrawchem/Makefile +++ b/science/xdrawchem/Makefile @@ -1,31 +1,32 @@ PORTNAME= xdrawchem DISTVERSION= 1.11.1-2 +PORTREVISION= 1 CATEGORIES= science MAINTAINER= yuri@FreeBSD.org COMMENT= Two-dimensional molecule drawing program WWW= https://sourceforge.net/projects/xdrawchem/ \ https://github.com/bryanherger/xdrawchem LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt LIB_DEPENDS= libopenbabel.so:science/openbabel USES= compiler:c++11-lang gl pkgconfig qmake qt:5 USE_QT= core gui network printsupport svg widgets xml buildtools:build USE_GL= gl USE_GITLAB= yes GL_SITE= https://salsa.debian.org GL_ACCOUNT= georgesk GL_TAGNAME= 48f2e4817be451550a2cd80263344642a8611b15 pre-configure: ${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|' \ ${WRKSRC}/xdrawchem.pro post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/${PORTNAME} .include