Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 474146) +++ head/science/Makefile (revision 474147) @@ -1,247 +1,248 @@ # $FreeBSD$ # COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit SUBDIR += MOOSE-neural-simulator SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += abinit SUBDIR += afni SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += atompaw SUBDIR += avogadro SUBDIR += bddsolve SUBDIR += bft SUBDIR += bodr SUBDIR += brian SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += clhep SUBDIR += colt SUBDIR += crf++ SUBDIR += dcl SUBDIR += devisor SUBDIR += dft_tools SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += eccodes SUBDIR += ecs SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += gwyddion SUBDIR += h5utils SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kalzium-kde4 SUBDIR += kst2 SUBDIR += lamprop SUBDIR += libaec + SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libint SUBDIR += libkml SUBDIR += liblinear SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += mpqc-mpich SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += openbabel SUBDIR += openkim SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-ReadGRIB SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += paje SUBDIR += paraview SUBDIR += pcmsolver SUBDIR += pnetcdf SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyQuante SUBDIR += py-ScientificPython SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-cdo SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-gsd SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-kinematics SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pymatgen SUBDIR += py-pymol SUBDIR += py-pyosf SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-quantities SUBDIR += py-rmf SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-spglib SUBDIR += py-tensorflow SUBDIR += py-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qcl SUBDIR += qtresistors SUBDIR += rdkit SUBDIR += rmf SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-rgeo SUBDIR += rubygem-rgeo-geojson SUBDIR += rubygem-rgeo-proj4 SUBDIR += rubygem-rgeo-shapefile SUBDIR += rubygem-ruby-dcl SUBDIR += rubygem-ruby-netcdf SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simlib SUBDIR += simsmith SUBDIR += spglib SUBDIR += step SUBDIR += step-kde4 SUBDIR += svmlight SUBDIR += szip SUBDIR += tfel SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim SUBDIR += vmd SUBDIR += voro++ SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include Index: head/science/libccp4/Makefile =================================================================== --- head/science/libccp4/Makefile (nonexistent) +++ head/science/libccp4/Makefile (revision 474147) @@ -0,0 +1,31 @@ +# $FreeBSD$ + +PORTNAME= libccp4 +DISTVERSION= 6.5.1 +CATEGORIES= science +MASTER_SITES= ftp://ftp.ccp4.ac.uk/opensource/ + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Protein X-ray crystallography toolkit + +LICENSE= GPLv3 LGPL3 +LICENSE_COMB= dual +LICENSE_FILE_GPLv3= ${WRKSRC}/COPYING +LICENSE_FILE_LGPL3= ${WRKSRC}/COPYING.LESSER + +LIB_DEPENDS= libmmdb2.so:science/mmdb2 + +USES= fortran gmake libtool localbase:ldflags +GNU_CONFIGURE= yes +CONFIGURE_ARGS= --enable-shared --disable-static +INSTALL_TARGET= install-strip +USE_LDCONFIG= yes + +CFLAGS+= -fPIC +FFLAGS+= -fPIC + +post-configure: + ${REINPLACE_CMD} -e 's| -Wl,--as-needed||; s| -Wl,--no-as-needed||' ${WRKSRC}/Makefile + ${REINPLACE_CMD} -e 's|^archive_cmds=|wl="-Wl,"; archive_cmds=|' ${WRKSRC}/libtool # wl is missing otherwise for some reason + +.include Property changes on: head/science/libccp4/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/libccp4/distinfo =================================================================== --- head/science/libccp4/distinfo (nonexistent) +++ head/science/libccp4/distinfo (revision 474147) @@ -0,0 +1,3 @@ +TIMESTAMP = 1531007069 +SHA256 (libccp4-6.5.1.tar.gz) = 280b473d950cdf8837ef66147ec581104298b892399bd856f13b096f2395dbe5 +SIZE (libccp4-6.5.1.tar.gz) = 947521 Property changes on: head/science/libccp4/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/libccp4/pkg-descr =================================================================== --- head/science/libccp4/pkg-descr (nonexistent) +++ head/science/libccp4/pkg-descr (revision 474147) @@ -0,0 +1,12 @@ +CCP4 exists to produce and support a world-leading, integrated suite of programs +that allows researchers to determine macromolecular structures by X-ray +crystallography, and other biophysical techniques. CCP4 aims to develop and +support the development of cutting edge approaches to experimental determination +and analysis of protein structure, and integrate these approaches into the +suite. CCP4 is a community based resource that supports the widest possible +researcher community, embracing academic, not for profit, and for profit +research. CCP4 aims to play a key role in the education and training of +scientists in experimental structural biology. It encourages the wide +dissemination of new ideas, techniques and practice. + +WWW: https://www.ccp4.ac.uk/ Property changes on: head/science/libccp4/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/libccp4/pkg-plist =================================================================== --- head/science/libccp4/pkg-plist (nonexistent) +++ head/science/libccp4/pkg-plist (revision 474147) @@ -0,0 +1,44 @@ +include/ccp4/ccp4_array.h +include/ccp4/ccp4_errno.h +include/ccp4/ccp4_file_err.h +include/ccp4/ccp4_fortran.h +include/ccp4/ccp4_general.h +include/ccp4/ccp4_parser.h +include/ccp4/ccp4_program.h +include/ccp4/ccp4_spg.h +include/ccp4/ccp4_sysdep.h +include/ccp4/ccp4_types.h +include/ccp4/ccp4_unitcell.h +include/ccp4/ccp4_utils.h +include/ccp4/ccp4_vars.h +include/ccp4/cmap_data.h +include/ccp4/cmap_errno.h +include/ccp4/cmap_header.h +include/ccp4/cmap_labels.h +include/ccp4/cmap_skew.h +include/ccp4/cmap_stats.h +include/ccp4/cmaplib.h +include/ccp4/cmaplib_f.h +include/ccp4/cmtzlib.h +include/ccp4/csymlib.h +include/ccp4/cvecmat.h +include/ccp4/library_file.h +include/ccp4/mtzdata.h +include/ccp4/overview.h +include/ccp4/pack_c.h +include/ccp4/w32mvs.h +lib/libccp4c.so +lib/libccp4c.so.0 +lib/libccp4c.so.0.0.0 +lib/libccp4f.so +lib/libccp4f.so.0 +lib/libccp4f.so.0.0.0 +libdata/pkgconfig/libccp4c.pc +libdata/pkgconfig/libccp4f.pc +share/atomsf.lib +share/atomsf_electron.lib +share/atomsf_neutron.lib +share/ccp4/ccp4-config.cmake +share/font84.ascii +share/syminfo.lib +share/symop.lib Property changes on: head/science/libccp4/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property