Index: head/benchmarks/clpeak/Makefile =================================================================== --- head/benchmarks/clpeak/Makefile (revision 516741) +++ head/benchmarks/clpeak/Makefile (revision 516742) @@ -1,35 +1,35 @@ # Created by: Johannes Dieterich # $FreeBSD$ PORTNAME= clpeak PORTVERSION= 1.0g20170524 CATEGORIES= benchmarks MAINTAINER= jmd@FreeBSD.org COMMENT= Benchmarking tool to measure peak capabilities of opencl devices LICENSE= PD LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= opencl>=0:devel/opencl LIB_DEPENDS= libOpenCL.so:devel/ocl-icd RUN_DEPENDS= opencl>=0:devel/opencl ONLY_FOR_ARCHS= amd64 USE_GITHUB= yes GH_ACCOUNT= krrishnarraj GH_TAGNAME= 75c8746 USE_LDCONFIG= yes +USES= cmake:insource gl USE_GL= gl -USES= cmake:insource CXXFLAGS+= -std=c++11 PLIST_FILES= bin/clpeak do-install: ${INSTALL_PROGRAM} ${WRKSRC}/clpeak ${STAGEDIR}${PREFIX}/bin/clpeak .include Index: head/benchmarks/glmark2/Makefile =================================================================== --- head/benchmarks/glmark2/Makefile (revision 516741) +++ head/benchmarks/glmark2/Makefile (revision 516742) @@ -1,34 +1,34 @@ # Created by: Alexey Dokuchaev # $FreeBSD$ PORTNAME= glmark2 PORTVERSION= 2014.03 PORTREVISION= 1 CATEGORIES= benchmarks MASTER_SITES= https://launchpadlibrarian.net/169075003/ MAINTAINER= danfe@FreeBSD.org COMMENT= Benchmark for OpenGL (ES) 2.0 LICENSE= GPLv3 LIB_DEPENDS= libpng.so:graphics/png -USES= jpeg localbase:ldflags pkgconfig waf +USES= gl jpeg localbase:ldflags pkgconfig waf USE_GL= egl gl glesv2 CONFIGURE_ARGS= --with-flavors=x11-gl,x11-glesv2 --no-opt --no-debug PORTDOCS= NEWS OPTIONS_DEFINE= DOCS post-patch: @${REINPLACE_CMD} -e "/lib/s/, 'dl'//" ${WRKSRC}/src/wscript_build @${REINPLACE_CMD} -e 's/GLMARK_VERSION/ &/' \ ${WRKSRC}/src/native-state-x11.cpp post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${PORTDOCS:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR} .include Index: head/biology/garlic/Makefile =================================================================== --- head/biology/garlic/Makefile (revision 516741) +++ head/biology/garlic/Makefile (revision 516742) @@ -1,52 +1,52 @@ # Created by: maho@FreeBSD.org # $FreeBSD$ PORTNAME= garlic PORTVERSION= 1.6 PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= http://www.zucic.org/sources/garlic-${PORTVERSION}/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= ports@FreeBSD.org COMMENT= Molecular viewer, editor, and visualization program -USES= gmake +USES= gmake xorg USE_XORG= x11 ALL_TARGET= # empty OPTIONS_DEFINE= DOCS EXAMPLES OPTIMIZED_CFLAGS .include .if ${PORT_OPTIONS:MDOCS} DISTFILES+= ${DISTNAME}-doc${EXTRACT_SUFX} .endif .if ${PORT_OPTIONS:MOPTIMIZED_CFLAGS} CFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations -malign-double .if (${ARCH} == "i386") CFLAGS+= -mfancy-math-387 -mpreferred-stack-boundary=3 .endif # i386 .endif post-patch: @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g ;\ s|%%CC%%|${CC}|g ; \ s|%%CFLAGS%%|${CFLAGS}|g' ${WRKSRC}/Makefile do-install: @${MKDIR} ${STAGEDIR}${DATADIR} ${STAGEDIR}${EXAMPLESDIR} \ ${STAGEDIR}${DOCSDIR} ${WRKDIR}/doc ${INSTALL_PROGRAM} ${WRKSRC}/garlic ${STAGEDIR}${PREFIX}/bin ${INSTALL_DATA} ${WRKSRC}/.garlicrc ${STAGEDIR}${DATADIR} ${INSTALL_DATA} ${WRKSRC}/residues.pdb ${STAGEDIR}${DATADIR} ${INSTALL_DATA} ${WRKSRC}/*.pdb ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/*.script ${STAGEDIR}${EXAMPLESDIR} (cd ${WRKDIR}/doc ; \ ${TAR} -xzf ${DISTDIR}/${DISTNAME}-doc${EXTRACT_SUFX} ) ${TAR} -C ${WRKDIR}/doc/${DISTNAME} -cf - . | \ ${TAR} -C ${STAGEDIR}${DOCSDIR} -xf - .include Index: head/biology/molden/Makefile =================================================================== --- head/biology/molden/Makefile (revision 516741) +++ head/biology/molden/Makefile (revision 516742) @@ -1,76 +1,76 @@ # Created by: Ryo MIYAMOTO # $FreeBSD$ PORTNAME= molden DISTVERSION= 5.8.2 PORTREVISION= 3 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/ DISTNAME= ${PORTNAME}${PORTVERSION} MAINTAINER= jmd@FreeBSD.org COMMENT= Display molecular orbitals and electron densities in 2D and 3D LICENSE= Molden LICENSE_NAME= Molden LICENSE_FILE= ${WRKSRC}/CopyRight LICENSE_PERMS= auto-accept RESTRICTED= free for academic, non profit usage; do not re-distribute source and executable. WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION:R} -USES= fortran gl gmake +USES= fortran gl gmake xorg USE_XORG= x11 USE_GL= gl glu MAKEFILE= makefile MAKE_JOBS_UNSAFE=yes CFLAGS+= -D${OPSYS:tu} -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 \ -I${LOCALBASE}/include -Wno-return-type PORTDOCS= * PORTDATA= * PLIST_FILES= bin/ambfor bin/gmolden bin/molden bin/surf PORTSCOUT= limit:^5\.0\. OPTIONS_DEFINE= DATA DOCS OPTIONS_DEFAULT= DATA post-patch: @${REINPLACE_CMD} -e \ 's|^CC |#CC | ; \ s|^FC |#FC | ; \ s|/usr/X11R6|${LOCALBASE}| ; \ s|$$(LIBS)|$$(LIBS) $$(LDFLAGS)| ; \ s|-lXmu|| ; \ /depend/s|^|#|' ${WRKSRC}/makefile post-configure: @${ECHO_MSG} "********************" @${ECHO_MSG} "** If you want to use a larger MOLDEN," @${ECHO_MSG} "** edit change_parameter.sh and run it," @${ECHO_MSG} "** before \'make build\'." @${ECHO_MSG} "********************" do-install: .for i in molden gmolden (cd ${WRKSRC} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}${PREFIX}/bin) .endfor .for i in ambfor surf (cd ${WRKSRC}/${i} && ${INSTALL_PROGRAM} ${i} ${STAGEDIR}/${PREFIX}/bin) .endfor do-install-DATA-on: @${MKDIR} ${STAGEDIR}${DATADIR}/test (cd ${WRKSRC}/test && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/test) ${MKDIR} ${STAGEDIR}${DATADIR}/utils (cd ${WRKSRC}/utils && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR}/utils) do-install-DOCS-on: ${MKDIR} ${STAGEDIR}${DOCSDIR} (cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR}) .include Index: head/biology/ncbi-cxx-toolkit/Makefile =================================================================== --- head/biology/ncbi-cxx-toolkit/Makefile (revision 516741) +++ head/biology/ncbi-cxx-toolkit/Makefile (revision 516742) @@ -1,32 +1,32 @@ # $FreeBSD$ PORTNAME= ncbi-cxx-toolkit DISTVERSION= 21_0_0 PORTREVISION= 2 CATEGORIES= biology science devel MASTER_SITES= ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2018/Apr_2_2018/ DISTNAME= ncbi_cxx--${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= NCBI C++ Toolkit LICENSE= PD LICENSE_FILE= ${WRKSRC}/doc/public/LICENSE LIB_DEPENDS= libpcre.so:devel/pcre RUN_DEPENDS= bash:shells/bash -USES= compiler:c++11-lang gmake mysql perl5 python shebangfix ssl +USES= compiler:c++11-lang gmake mysql perl5 python shebangfix ssl xorg SHEBANG_FILES= src/app/blast/get_species_taxids.sh src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl src/app/winmasker/windowmasker_2.2.22_adapter.py USE_XORG= x11 xpm GNU_CONFIGURE= yes CONFIGURE_ARGS= --without-debug --with-dll --without-static post-install: # autoplist: thousands of files @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/run_with_lock @cd ${STAGEDIR}${PREFIX} && \ ${RMDIR} include/ncbi-tools++/algo/blast/bl2api include/ncbi-tools++/objtools/test && \ ${FIND} * -type f -or -type l >> ${TMPPLIST} .include Index: head/biology/phylip/Makefile =================================================================== --- head/biology/phylip/Makefile (revision 516741) +++ head/biology/phylip/Makefile (revision 516742) @@ -1,49 +1,49 @@ # Created by: David A. Bader # $FreeBSD$ PORTNAME= phylip PORTVERSION= 3.697 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= http://evolution.gs.washington.edu/phylip/download/ MAINTAINER= ports@FreeBSD.org COMMENT= Phylogeny Inference Package LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/src/COPYRIGHT BUILD_DEPENDS= bash:shells/bash BUILD_WRKSRC= ${WRKSRC}/src INSTALL_WRKSRC= ${WRKSRC}/src -USES= gmake +USES= gmake xorg USE_XORG= x11 xaw xt MAKEFILE= Makefile.unx MAKE_ARGS= CC="${CC}" CFLAGS="${CFLAGS} -DUNX" \ DFLAGS="${CFLAGS} -DX -I${LOCALBASE}/include" \ DLIBS="-L${LOCALBASE}/lib -lX11 -lXaw -lXt -lm" USE_LDCONFIG= yes PORTDOCS= * OPTIONS_DEFINE= DOCS post-install: @cd ${WRKSRC}/exe && \ ${FIND} . -maxdepth 1 -not -type d -not -name '*.jar' \ -not -name '*.unx' -not -name 'font*' -not -name '*.so' \ | ${XARGS} -J % ${INSTALL_PROGRAM} % ${STAGEDIR}${PREFIX}/bin @cd ${WRKSRC}/exe && \ ${FIND} . -maxdepth 1 -not -type d -name "*.so" \ | ${XARGS} -J % ${INSTALL_LIB} % ${STAGEDIR}${PREFIX}/lib @${MKDIR} ${STAGEDIR}${DATADIR} @cd ${WRKSRC}/exe && \ ${FIND} . -maxdepth 1 -not -type d -name 'font*' \ | ${XARGS} -J % ${INSTALL_DATA} % ${STAGEDIR}${DATADIR} @${MKDIR} ${STAGEDIR}${DOCSDIR} @(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . \ ${STAGEDIR}${DOCSDIR}) .include Index: head/biology/protomol/Makefile =================================================================== --- head/biology/protomol/Makefile (revision 516741) +++ head/biology/protomol/Makefile (revision 516742) @@ -1,52 +1,53 @@ # Created by: Sangwoo Shim # $FreeBSD$ PORTNAME= protomol PORTVERSION= 2.0.3 PORTREVISION= 14 CATEGORIES= biology MASTER_SITES= SF/${PORTNAME}/ProtoMol/${PORTVERSION} DISTFILES= ${DISTNAME}-tar.gz MAINTAINER= ports@FreeBSD.org COMMENT= OO, component based, framework for molecular dynamics (MD) simulations LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libpng.so:graphics/png \ libtiff.so:graphics/tiff -USES= jpeg shebangfix +USES= jpeg shebangfix xorg USE_CXXSTD= c++98 SHEBANG_FILES= examples/butane_4/procDihedralFile.awk \ examples/butane_4/cleanOutput.bash \ examples/butane_4/runButaneResults.sh \ examples/butane_4/runButaneTests.sh SHEBANG_LANG= awk awk_OLD_CMD= /usr/bin/gawk awk_CMD= /usr/bin/awk # base awk works fine in this case GNU_CONFIGURE= yes USE_XORG= xmu xt sm ice xext x11 xi # Hack to cure a misbehavior of the configure script CONFIGURE_ARGS+= --without-irix_mipspro_mpi CPPFLAGS+= -I${LOCALBASE}/include CXXFLAGS+= -L${LOCALBASE}/lib WRKSRC= ${WRKDIR}/${PORTNAME} OPTIONS_DEFINE= GLUT EXAMPLES OPTIONS_DEFAULT= GLUT GLUT_CONFIGURE_ON= --with-glut=yes +GLUT_USES= gl GLUT_USE= GL=glut GLUT_CONFIGURE_OFF= --with-glut=no post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} cd ${WRKSRC}/examples ; \ ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR} "! -name .cvsignore" .include Index: head/biology/seaview/Makefile =================================================================== --- head/biology/seaview/Makefile (revision 516741) +++ head/biology/seaview/Makefile (revision 516742) @@ -1,53 +1,53 @@ # Created by: frankch@waru.life.nthu.edu.tw # $FreeBSD$ PORTNAME= seaview PORTVERSION= 4.7 PORTEPOCH= 1 CATEGORIES= biology MASTER_SITES= ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/ DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= bofh@FreeBSD.org COMMENT= Multiple DNA/protein sequence alignment editor LICENSE= GPLv3 LIB_DEPENDS= libfltk.so:x11-toolkits/fltk \ libfontconfig.so:x11-fonts/fontconfig \ libpng.so:graphics/png PORTSCOUT= skipv:4.6.1.3 WRKSRC= ${WRKDIR}/${PORTNAME} -USES= gmake jpeg +USES= gmake jpeg xorg USE_XORG= x11 xcursor xext xfixes xft xinerama xrender MAKE_ENV= HELPFILE='-DDEFAULT_HELPFILE=\"${DATADIR}/seaview.html\"' \ PHYMLNAME='-DPHYMLNAME=\"phyml\"' \ IFLTK='-I${LOCALBASE}/include' \ LFLTK='-L${LOCALBASE}/lib' \ USE_XFT='-DUSE_XFT' \ OPT="${CFLAGS}" ALL_TARGET= ${PORTNAME} DESKTOP_ENTRIES="SeaView" "" "${PREFIX}/share/pixmaps/seaview.xpm" "seaview" \ "Biology;Science;" true post-patch: ${REINPLACE_CMD} -e \ 's|^\(CC\) |#\1 | ; s|-ldl || ; \ s|^\(CXX\) |#\1 |' ${WRKSRC}/Makefile do-install: (cd ${WRKSRC} && ${INSTALL_PROGRAM} seaview \ ${STAGEDIR}${PREFIX}/bin) (cd ${WRKSRC} && ${INSTALL_MAN} seaview.1 \ ${STAGEDIR}${MANPREFIX}/man/man1) ${MKDIR} ${STAGEDIR}${DATADIR} (cd ${WRKSRC} && ${INSTALL_DATA} seaview.html \ ${STAGEDIR}${DATADIR}) (cd ${WRKSRC} && ${INSTALL_DATA} seaview.xpm \ ${STAGEDIR}${PREFIX}/share/pixmaps) .include Index: head/biology/seqtools/Makefile =================================================================== --- head/biology/seqtools/Makefile (revision 516741) +++ head/biology/seqtools/Makefile (revision 516742) @@ -1,30 +1,30 @@ # $FreeBSD$ PORTNAME= seqtools PORTVERSION= 4.44.1 PORTREVISION= 4 CATEGORIES= biology MASTER_SITES= ftp://ftp.sanger.ac.uk/pub4/resources/software/seqtools/PRODUCTION/ MAINTAINER= pi@FreeBSD.org COMMENT= Tools for visualising sequence alignments LICENSE= GPLv3 LIB_DEPENDS= libcurl.so:ftp/curl \ libsqlite3.so:databases/sqlite3 \ libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 -USES= compiler:c++14-lang gettext libtool pkgconfig +USES= compiler:c++14-lang gettext gnome libtool pkgconfig xorg GNU_CONFIGURE= yes USE_GNOME= cairo gdkpixbuf2 gtk20 USE_XORG= x11 CFLAGS+= -I${LOCALBASE}/include LLD_UNSAFE= yes LDFLAGS+= -L${LOCALBASE}/lib -lexecinfo -lcurl -lsqlite3 -lm MAKE_JOBS_UNSAFE= yes OPTIONS_DEFINE= DOCS .include Index: head/biology/ugene/Makefile =================================================================== --- head/biology/ugene/Makefile (revision 516741) +++ head/biology/ugene/Makefile (revision 516742) @@ -1,72 +1,72 @@ # Created by: Hannes Hauswedell # $FreeBSD$ PORTNAME= ugene DISTVERSION= 1.31.0 PORTREVISION= 1 CATEGORIES= biology science MASTER_SITES= http://ugene.unipro.ru/downloads/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \ UniproUGENE_UserManual.pdf WorkflowDesigner_UserManual.pdf DIST_SUBDIR= ${PORTNAME} EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= h2+fbsdports@fsfe.org COMMENT= Free, open-source, cross-platform bioinformatics toolkit LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE.txt RUN_DEPENDS= bash:shells/bash BROKEN_aarch64= Fails to build: invokes x86 asm -USES= desktop-file-utils qmake qt:5 shared-mime-info +USES= desktop-file-utils gl qmake qt:5 shared-mime-info xorg USE_GL= gl glu USE_QT= buildtools_build linguisttools_build \ core gui network opengl printsupport script scripttools \ sql svg testlib webkit widgets xml \ imageformats_run USE_XORG= x11 xtst QMAKE_ARGS= INSTALL_PREFIX="${PREFIX}" UGENE_INSTALL_DATA="${DATADIR}" \ INSTALL_MANDIR="${MAN1PREFIX}/man" LRELEASE="${LRELEASE}" \ LUPDATE="${LUPDATE}" ALL_TARGET= release DOCSDIR= ${DATADIR}/manuals OPTIONS_DEFINE= DOCS OPENCL DOCS_DESC= Install official UGENE documentation (PDF) OPENCL_QMAKE_ON= UGENE_OPENCL_DETECTED=1 .include .if ${ARCH} == amd64 # XXX: need to manually tell the build we are on x64 QMAKE_ARGS+= CONFIG+=x64 .endif .if ${MACHINE_CPU:Msse2} QMAKE_ARGS+= UGENE_SSE2_DETECTED=1 .endif post-extract: @${MKDIR} ${WRKSRC}/data/manuals ${CP} -p ${_DISTDIR}/*.pdf ${WRKSRC}/data/manuals post-patch: # yes, bash is required, stuff will not execute with sh @${REINPLACE_CMD} -e 's|/bin/bash|/usr/bin/env bash|' \ ${WRKSRC}/src/gen_bin_script.cmd \ ${WRKSRC}/installer/_common_data/ugene @${REINPLACE_CMD} -e 's|-bit version|& for ${OPSYS}/${ARCH}|' \ ${WRKSRC}/src/ugeneui/src/main_window/AboutDialogController.cpp @${REINPLACE_CMD} 's, -lbreakpad,,' \ ${WRKSRC}/src/corelibs/U2Private/U2Private.pri \ ${WRKSRC}/src/plugins_checker/plugins_checker.pri \ ${WRKSRC}/src/ugenecl/ugenecl.pri \ ${WRKSRC}/src/ugeneui/ugeneui.pri .include Index: head/biology/viennarna/Makefile =================================================================== --- head/biology/viennarna/Makefile (revision 516741) +++ head/biology/viennarna/Makefile (revision 516742) @@ -1,42 +1,42 @@ # $FreeBSD$ PORTNAME= viennarna DISTVERSION= 2.4.13 PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ DISTNAME= ViennaRNA-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Alignment tools for the structural analysis of RNA LICENSE= ViennaRNALicense LICENSE_NAME= Vienna RNA License LICENSE_FILE= ${WRKSRC}/COPYING LICENSE_PERMS= auto-accept dist-mirror pkg-mirror BUILD_DEPENDS= bash:shells/bash \ libgd>0:graphics/gd # for the static lib LIB_DEPENDS= libgmp.so:math/gmp \ libgsl.so:math/gsl \ libmpfr.so:math/mpfr -USES= autoreconf compiler:c++11-lang gmake libtool localbase perl5 pkgconfig # w/out autoreconf -lstdc++ is present in configure and Makefiles and this causes link failure +USES= autoreconf compiler:c++11-lang gmake libtool localbase perl5 pkgconfig xorg # w/out autoreconf -lstdc++ is present in configure and Makefiles and this causes link failure USE_XORG= x11 xext # only for build GNU_CONFIGURE= yes CONFIGURE_SHELL= ${PREFIX}/bin/bash CONFIGURE_ARGS= --enable-shared --disable-static --with-gsl --with-cluster --with-kinwalker --enable-mpfr --without-python --without-python3 --without-perl INFO= RNAlib DATASDIR= ${PREFIX}/share/ViennaRNA DOCSDIR= ${PREFIX}/share/doc/ViennaRNA EXAMPLESDIR= ${PREFIX}/share/examples/ViennaRNA OPTIONS_DEFINE= DOCS EXAMPLES PORTDOCS= * PORTEXAMPLES= * .include