Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 492828) +++ head/science/Makefile (revision 492829) @@ -1,323 +1,324 @@ # $FreeBSD$ # 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 += agrum SUBDIR += aircraft-datcom SUBDIR += antioch SUBDIR += atom SUBDIR += atompaw SUBDIR += avogadro SUBDIR += avogadro2 SUBDIR += avogadrolibs SUBDIR += bagel SUBDIR += bddsolve SUBDIR += berkeleygw 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 += chrono SUBDIR += clhep SUBDIR += clipper SUBDIR += code_saturne SUBDIR += colt SUBDIR += coordgenlibs SUBDIR += coot SUBDIR += cp2k SUBDIR += crf++ SUBDIR += dalton SUBDIR += datawarrior SUBDIR += dcl SUBDIR += devisor SUBDIR += dft_tools SUBDIR += dftbplus SUBDIR += dkh SUBDIR += dlib-cpp SUBDIR += dlpoly-classic SUBDIR += drawxtl SUBDIR += eccodes SUBDIR += elk SUBDIR += epte SUBDIR += erd SUBDIR += erkale SUBDIR += erkale-pseudopotentials SUBDIR += esys-particle SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fleur SUBDIR += fsom SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += gabedit SUBDIR += gamess-us SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gpaw-setups SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += gwyddion SUBDIR += h5utils SUBDIR += h5z-zfp SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += healpix SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jdftx SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kst2 SUBDIR += lammps SUBDIR += lamprop SUBDIR += latte SUBDIR += libaec SUBDIR += libccp4 SUBDIR += libcint SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libgridxc SUBDIR += libint SUBDIR += libint2 SUBDIR += libkml SUBDIR += liblinear SUBDIR += libmsym SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libssm SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += liggghts SUBDIR += lm SUBDIR += luscus SUBDIR += madness SUBDIR += maeparser SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += mcxtrace-comps SUBDIR += mdynamix SUBDIR += medit SUBDIR += meep SUBDIR += metaf2xml SUBDIR += metaphysicl SUBDIR += minc2 SUBDIR += mmdb2 SUBDIR += mmtf SUBDIR += mol2ps SUBDIR += molgif + SUBDIR += molscript SUBDIR += molsketch SUBDIR += mpb SUBDIR += mpqc SUBDIR += msms SUBDIR += multiwfn SUBDIR += namd SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += nwchem SUBDIR += nwchem-data SUBDIR += octopus SUBDIR += openbabel SUBDIR += openkim SUBDIR += openmx SUBDIR += opensim-core SUBDIR += openstructure 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-GPy SUBDIR += py-GPyOpt SUBDIR += py-MDAnalysis SUBDIR += py-MDAnalysisTests SUBDIR += py-OpenFermion SUBDIR += py-PyFR SUBDIR += py-PyQuante SUBDIR += py-ScientificPython SUBDIR += py-SimpleSpectral SUBDIR += py-abipy SUBDIR += py-asdf SUBDIR += py-ase SUBDIR += py-avogadrolibs SUBDIR += py-cdo SUBDIR += py-chempy SUBDIR += py-coards SUBDIR += py-dlib SUBDIR += py-gpaw SUBDIR += py-gsd SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-kinematics SUBDIR += py-lifelines SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-mmtf-python SUBDIR += py-molmod SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-oddt SUBDIR += py-openpiv SUBDIR += py-paida SUBDIR += py-paramz SUBDIR += py-phono3py SUBDIR += py-phonopy SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pygeodesy 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-rmsd 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-veusz SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qbox SUBDIR += qcl SUBDIR += qmcpack SUBDIR += qtresistors SUBDIR += quantum-espresso SUBDIR += quantum-espresso-pseudopotentials SUBDIR += qwalk 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 += scidavis SUBDIR += siesta SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simbody SUBDIR += simint SUBDIR += simlib SUBDIR += simsmith SUBDIR += sparta SUBDIR += spglib SUBDIR += step SUBDIR += svmlight SUBDIR += szip SUBDIR += teem SUBDIR += tfel SUBDIR += tinker SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim SUBDIR += vipster SUBDIR += vmd SUBDIR += voro++ SUBDIR += wannier90 SUBDIR += wxmacmolplt SUBDIR += xcrysden SUBDIR += xdrawchem SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol SUBDIR += yoda .include Index: head/science/molscript/Makefile =================================================================== --- head/science/molscript/Makefile (nonexistent) +++ head/science/molscript/Makefile (revision 492829) @@ -0,0 +1,47 @@ +# $FreeBSD$ + +PORTNAME= MolScript +DISTVERSION= 2.1.2 +CATEGORIES= science + +MAINTAINER= yuri@FreeBSD.org +COMMENT= Display 3D molecules in schematic and detailed representations + +LICENSE= MIT +LICENSE_FILE= ${WRKSRC}/../LICENSE.txt + +LIB_DEPENDS= libpng16.so:graphics/png +RUN_DEPENDS= render:graphics/raster3d # molscript use requires the executable 'render' to be present + +USES= gl gmake jpeg localbase:ldflags +USE_GITHUB= yes +GH_ACCOUNT= pekrau +GH_TAGNAME= 280abee +USE_GL= gl glu glut +USE_XORG= x11 xext xmu + +MAKEFILE= Makefile.complete + +MAKE_ARGS= CC=${CC} COPT="${CFLAGS}" +CFLAGS+= -I${FILESDIR} +WRKSRC_SUBDIR= code + +BINARY_ALIAS= make=${MAKE_CMD} + +PROGS= ${PORTNAME:tl} molauto + +PLIST_FILES= ${PROGS:S/^/bin\//} + +OPTIONS_DEFINE= DOCS + +PORTDOCS= * + +do-install: +.for e in ${PROGS} + ${INSTALL_PROGRAM} ${WRKSRC}/../${e} ${STAGEDIR}${PREFIX}/bin +.endfor + +do-install-DOCS-on: + cd ${WRKSRC}/../docs && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR} + +.include Property changes on: head/science/molscript/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/molscript/distinfo =================================================================== --- head/science/molscript/distinfo (nonexistent) +++ head/science/molscript/distinfo (revision 492829) @@ -0,0 +1,3 @@ +TIMESTAMP = 1550040979 +SHA256 (pekrau-MolScript-2.1.2-280abee_GH0.tar.gz) = 701f31aa42e5aabe327ab417a7230d394e5511f82d0f43e93ba1d3989719dbe2 +SIZE (pekrau-MolScript-2.1.2-280abee_GH0.tar.gz) = 4749679 Property changes on: head/science/molscript/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/molscript/files/glutbitmap.h =================================================================== --- head/science/molscript/files/glutbitmap.h (nonexistent) +++ head/science/molscript/files/glutbitmap.h (revision 492829) @@ -0,0 +1,32 @@ +#ifndef __glutbitmap_h__ +#define __glutbitmap_h__ + +/* Copyright (c) Mark J. Kilgard, 1994, 1998. */ + +/* This program is freely distributable without licensing fees + and is provided without guarantee or warrantee expressed or + implied. This program is -not- in the public domain. */ + +#define GLUT_NO_LIB_PRAGMA /* Avoid auto library linking when building + the GLUT library itself. */ +#include + +typedef struct { + const GLsizei width; + const GLsizei height; + const GLfloat xorig; + const GLfloat yorig; + const GLfloat advance; + const GLubyte *bitmap; +} BitmapCharRec, *BitmapCharPtr; + +typedef struct { + const char *name; + const int num_chars; + const int first; + const BitmapCharRec * const *ch; +} BitmapFontRec, *BitmapFontPtr; + +typedef void *GLUTbitmapFont; + +#endif /* __glutbitmap_h__ */ Property changes on: head/science/molscript/files/glutbitmap.h ___________________________________________________________________ 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/molscript/files/patch-Makefile.complete =================================================================== --- head/science/molscript/files/patch-Makefile.complete (nonexistent) +++ head/science/molscript/files/patch-Makefile.complete (revision 492829) @@ -0,0 +1,70 @@ +--- Makefile.complete.orig 2017-01-16 17:36:29 UTC ++++ Makefile.complete +@@ -28,8 +28,8 @@ SHELL = /bin/sh + + # OpenGL and GLUT for X (UNIX). + # Must be modified for Windows 95/NT. <--- +-GLUTDIR = $(FREEWAREDIR)/glut +-GLUTLINK = $(GLUTDIR)/lib/glut/libglut.a -lGLU -lGL -lXmu -lXext -lX11 ++GLUTDIR = $(PREFIX) ++GLUTLINK = $(GLUTDIR)/lib/libglut.so -lGLU -lGL -lXmu -lXext -lX11 + OPENGLFLAG = -DOPENGL_SUPPORT -I$(GLUTDIR)/include + OPENGLOBJ = opengl.o + OPENGLCLIBOBJ = ogl_utils.o ogl_body.o ogl_bitmap_character.o +@@ -40,26 +40,26 @@ IMAGEOBJ = image.o eps_img.o sgi_img.o + + # JPEG image file format; requires the JPEG library. + # Comment out these lines if the JPEG library is not available. <--- +-JPEGDIR = $(FREEWAREDIR)/jpeg +-JPEGLINK = $(JPEGDIR)/libjpeg.a +-JPEGFLAG = -DJPEG_SUPPORT -I$(JPEGDIR) ++JPEGDIR = $(PREFIX) ++JPEGLINK = $(JPEGDIR)/lib/libjpeg.so ++JPEGFLAG = -DJPEG_SUPPORT -I$(JPEGDIR)/include + JPEGOBJ = jpeg_img.o + + # PNG image file format; requires the PNG library and the zlib library. + # Comment out these lines if the PNG and zlib libraries are not available. <--- +-ZLIBDIR = $(FREEWAREDIR)/zlib +-ZLIBLINK = $(ZLIBDIR)/libz.a +-PNGDIR = $(FREEWAREDIR)/libpng +-PNGLINK = $(PNGDIR)/libpng.a +-PNGFLAG = -DPNG_SUPPORT -I$(PNGDIR) -I$(ZLIBDIR) ++ZLIBDIR = /usr ++ZLIBLINK = $(ZLIBDIR)/lib/libz.so ++PNGDIR = $(PREFIX) ++PNGLINK = $(PNGDIR)/lib/libpng.so ++PNGFLAG = -DPNG_SUPPORT -I$(PNGDIR)/include -I$(ZLIBDIR)/include + PNGOBJ = png_img.o + + # GIF image file format; requires the gd 1.3 library. + # Comment out these lines if the gd 1.3 library is not available. <--- +-GIFDIR = $(FREEWAREDIR)/gd +-GIFLINK = $(GIFDIR)/libgd.a +-GIFFLAG = -DGIF_SUPPORT -I$(GIFDIR) +-GIFOBJ = gif_img.o ++#GIFDIR = $(FREEWAREDIR)/gd ++#GIFLINK = $(GIFDIR)/libgd.a ++#GIFFLAG = -DGIF_SUPPORT -I$(GIFDIR) ++#GIFOBJ = gif_img.o + + # SGI IRIX's C compiler. + CC = cc -32 +@@ -67,7 +67,7 @@ CC = cc -32 + COPT = -O1 + # Correctness flags: + #CCHECK = -ansi -fullwarn -g -DSELECT_DEBUG +-CCHECK = -ansi -fullwarn ++CCHECK = -ansi + #CCHECK = -ansi -fullwarn -DNDEBUG + + # General cc compile flags. +@@ -95,7 +95,7 @@ clean: + + #------------------------------------------------------------ + $(MOLSCRIPT): $(OBJ) clib/clib.a +- $(CC) -o $(MOLSCRIPT) $(COPT) $(OBJ) $(YLIB) clib/clib.a \ ++ $(CC) -o $(MOLSCRIPT) $(COPT) $(OBJ) $(YLIB) $(LDFLAGS) clib/clib.a \ + $(GLUTLINK) $(JPEGLINK) $(PNGLINK) $(GIFLINK) $(ZLIBLINK) -lm + + molscript.tab.o: molscript.tab.c molscript.tab.h Property changes on: head/science/molscript/files/patch-Makefile.complete ___________________________________________________________________ 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/molscript/files/patch-clib_ogl__bitmap__character.c =================================================================== --- head/science/molscript/files/patch-clib_ogl__bitmap__character.c (nonexistent) +++ head/science/molscript/files/patch-clib_ogl__bitmap__character.c (revision 492829) @@ -0,0 +1,11 @@ +--- clib/ogl_bitmap_character.c.orig 2019-02-13 05:26:19 UTC ++++ clib/ogl_bitmap_character.c +@@ -23,7 +23,7 @@ + + #include + +-#include <../lib/glut/glutbitmap.h> ++#include "glutbitmap.h" + + + /*------------------------------------------------------------*/ Property changes on: head/science/molscript/files/patch-clib_ogl__bitmap__character.c ___________________________________________________________________ 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/molscript/files/patch-png__img.c =================================================================== --- head/science/molscript/files/patch-png__img.c (nonexistent) +++ head/science/molscript/files/patch-png__img.c (revision 492829) @@ -0,0 +1,19 @@ +--- png_img.c.orig 2017-01-16 17:36:29 UTC ++++ png_img.c +@@ -19,6 +19,7 @@ + #include + + #include ++#include + + #include "clib/str_utils.h" + #include "clib/dynstring.h" +@@ -69,7 +70,7 @@ pngi_first_plot (void) + info_ptr = png_create_info_struct (png_ptr); + if (info_ptr == NULL) + yyerror ("png_img: could not create PNG info structure"); +- if (setjmp (png_ptr->jmpbuf)) yyerror ("png_img: could not setjmp"); ++ if (setjmp (png_jmpbuf(png_ptr))) yyerror ("png_img: could not setjmp"); + + png_init_io (png_ptr, outfile); + png_set_compression_level (png_ptr, compression_level); Property changes on: head/science/molscript/files/patch-png__img.c ___________________________________________________________________ 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/molscript/pkg-descr =================================================================== --- head/science/molscript/pkg-descr (nonexistent) +++ head/science/molscript/pkg-descr (revision 492829) @@ -0,0 +1,7 @@ +MolScript is a program for displaying molecular 3D structures, such as proteins, +in both schematic and detailed representations. + +Output formats: PostScript, Raster3D, VRML 2.0, interactive OpenGL, SGI +(aka RGB), JPEG, EPS, PNG, GIF. + +WWW: http://avatar.se/molscript/molscript.html Property changes on: head/science/molscript/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