Index: head/audio/praat/Makefile =================================================================== --- head/audio/praat/Makefile (revision 460451) +++ head/audio/praat/Makefile (revision 460452) @@ -1,44 +1,43 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= praat PORTVERSION= 5.4.08 DISTVERSIONPREFIX= v PORTREVISION= 3 CATEGORIES= audio science -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Phonetics by Computer LICENSE= GPLv2 BROKEN_powerpc64= fails to compile: cc1plus: unrecognized command line option "-std=gnu++11" USE_GITHUB= yes DOS2UNIX_REGEX= .*Makefile USES= dos2unix iconv pkgconfig USE_GNOME= gtk20 MAKEFILE= makefile PLIST_FILES= bin/praat man/man1/praat.1.gz post-patch: @${FIND} ${WRKSRC} -name Makefile -exec \ ${REINPLACE_CMD} -e 's|^CFLAGS =|CFLAGS +=|' {} \; @${FIND} ${WRKSRC} -name Makefile -exec \ ${REINPLACE_CMD} -e 's|^CPPFLAGS =|CPPFLAGS +=|' {} \; @${CP} ${FILESDIR}/makefile.defs.freebsd.alsa \ ${WRKSRC}/makefile.defs @${REINPLACE_CMD} -e 's|%%WRKSRC%%|${WRKSRC}|g' \ -e 's|%%LOCALBASE%%|${LOCALBASE}|g' \ ${WRKSRC}/makefile.defs @${REINPLACE_CMD} -e 's| log2| NUMlog2|g' \ -e 's|feof (f)|feof (f.get_ptr())|g' \ -e 's|ferror (f)|ferror (f.get_ptr())|g' \ ${WRKSRC}/dwtools/Sound_extensions.cpp \ ${WRKSRC}/fon/Sound_files.cpp do-install: ${INSTALL_PROGRAM} ${WRKSRC}/praat ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${FILESDIR}/praat.1 ${STAGEDIR}${PREFIX}/man/man1 .include Index: head/biology/bowtie/Makefile =================================================================== --- head/biology/bowtie/Makefile (revision 460451) +++ head/biology/bowtie/Makefile (revision 460452) @@ -1,47 +1,46 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= bowtie PORTVERSION= 1.1.2 PORTREVISION= 4 DISTVERSIONPREFIX= v CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Ultrafast, memory-efficient short read aligner LICENSE= ART10 # May also work on other 64-bit platforms, but untested ONLY_FOR_ARCHS= amd64 # FIXME: bowtie-align intermittently dumps core when compiled with clang # GCC 4.2 does not provide good performance USE_GCC= yes USES= gmake perl5 python:run shebangfix USE_PERL5= run SHEBANG_FILES= scripts/*.pl bowtie bowtie-build \ bowtie-inspect USE_GITHUB= yes GH_ACCOUNT= BenLangmead post-install: ${MKDIR} ${STAGEDIR}${DATADIR}/scripts ${INSTALL_SCRIPT} \ ${WRKSRC}/bowtie \ ${WRKSRC}/bowtie-build \ ${WRKSRC}/bowtie-inspect \ ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} \ ${WRKSRC}/scripts/*.sh \ ${WRKSRC}/scripts/*.pl \ ${STAGEDIR}${DATADIR}/scripts cd ${WRKSRC} && ${COPYTREE_SHARE} \ 'genomes indexes reads' \ ${STAGEDIR}${DATADIR} cd ${WRKSRC}/doc && ${COPYTREE_SHARE} \ \* \ ${STAGEDIR}${DOCSDIR} ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/*-[sl] .include Index: head/biology/bwa/Makefile =================================================================== --- head/biology/bwa/Makefile (revision 460451) +++ head/biology/bwa/Makefile (revision 460452) @@ -1,43 +1,42 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= bwa PORTVERSION= 0.7.17 DISTVERSIONPREFIX=v CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Burrows-Wheeler sequence aligner LICENSE= GPLv3 # From 0.7.9a: Recheck for 0.7.17. BROKEN_aarch64= fails to compile: invalid conversion between vector type and integer type BROKEN_armv6= fails to compile: invalid conversion between vector type and integer type BROKEN_armv7= fails to compile: invalid conversion between vector type and integer type BROKEN_mips= fails to compile: cc1: unrecognized command line option "-msse2" BROKEN_mips64= fails to compile: cc1: unrecognized command line option "-msse2" BROKEN_powerpc64= fails to compile: ksw.c: emmintrin.h: No such file or directory USES= gmake perl5 shebangfix tar:bzip2 SHEBANG_FILES= qualfa2fq.pl xa2multi.pl USE_PERL5= run USE_GITHUB= yes GH_ACCOUNT= lh3 PLIST_FILES= bin/bwa bin/qualfa2fq.pl bin/xa2multi.pl man/man1/bwa.1.gz .include .if ${ARCH} == amd64 || ${ARCH} == i386 # Avoid #error in emmintrin.h CFLAGS+= -msse2 .endif do-install: ${INSTALL_PROGRAM} ${WRKSRC}/bwa ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${WRKSRC}/*.pl ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/*.1 ${STAGEDIR}${MAN1PREFIX}/man/man1 .include Index: head/biology/cd-hit/Makefile =================================================================== --- head/biology/cd-hit/Makefile (revision 460451) +++ head/biology/cd-hit/Makefile (revision 460452) @@ -1,38 +1,37 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= cd-hit PORTVERSION= 4.6.6 PORTREVISION= 2 DISTVERSIONPREFIX= V CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Clustering and comparing protein or nucleotide sequences LICENSE= GPLv2 USE_GITHUB= yes GH_ACCOUNT= weizhongli GH_PROJECT= cdhit USES= compiler:openmp gmake shebangfix SHEBANG_FILES= ${WRKSRC}/*.pl MAKE_FLAGS= openmp=yes post-patch: @${REINPLACE_CMD} \ -e 's|g++|${CXX}|g' \ -e 's|\$$(PREFIX)|$${DESTDIR}$${PREFIX}/bin|g' \ ${WRKSRC}/${MAKEFILE} @${REINPLACE_CMD} \ -e 's|/bin/bash|${LOCALBASE}/bin/bash|g' \ ${WRKSRC}/*.pl post-install: @cd ${STAGEDIR}${PREFIX}/bin && \ ${STRIP_CMD} cd-hit cd-hit-2d cd-hit-454 \ cd-hit-div cd-hit-est cd-hit-est-2d .include Index: head/biology/cdbfasta/Makefile =================================================================== --- head/biology/cdbfasta/Makefile (revision 460451) +++ head/biology/cdbfasta/Makefile (revision 460452) @@ -1,24 +1,24 @@ # Created by: Dan Siercks # $FreeBSD$ PORTNAME= cdbfasta PORTVERSION= 2010.07.22 CATEGORIES= biology MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Fast indexing and retrieval of FASTA records from flat file databases # LICENSE= unspecified WRKSRC= ${WRKDIR}/${PORTNAME} USES= gmake PLIST_FILES= bin/cdbfasta bin/cdbyank do-install: ${INSTALL_PROGRAM} ${WRKSRC}/cdbfasta ${STAGEDIR}${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/cdbyank ${STAGEDIR}${PREFIX}/bin .include Index: head/biology/fastool/Makefile =================================================================== --- head/biology/fastool/Makefile (revision 460451) +++ head/biology/fastool/Makefile (revision 460452) @@ -1,31 +1,30 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= fastool PORTVERSION= 0.1.4 CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Simple and quick FastQ and FastA tool for file reading and conversion LICENSE= BSD2CLAUSE USE_GITHUB= yes GH_ACCOUNT= fstrozzi GH_PROJECT= Fastool PLIST_FILES= bin/fastool CFLAGS+= -std=c99 post-patch: ${REINPLACE_CMD} \ -e 's|CC *=|CC ?=|g' \ -e 's|CFLAGS *=|CFLAGS ?=|g' \ ${WRKSRC}/Makefile do-install: ${INSTALL_PROGRAM} ${WRKSRC}/fastool \ ${STAGEDIR}${PREFIX}/bin .include Index: head/biology/fastx-toolkit/Makefile =================================================================== --- head/biology/fastx-toolkit/Makefile (revision 460451) +++ head/biology/fastx-toolkit/Makefile (revision 460452) @@ -1,25 +1,24 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= fastx_toolkit PORTVERSION= 0.0.14 CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= CLI tools for Short-Reads FASTA/FASTQ files preprocessing LICENSE= AGPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libgtextutils.so:biology/libgtextutils USES= autoreconf libtool perl5 pkgconfig shebangfix USE_PERL5= run SHEBANG_FILES= scripts/*.pl USE_GITHUB= yes GH_ACCOUNT= agordon GNU_CONFIGURE= yes .include Index: head/biology/gmap/Makefile =================================================================== --- head/biology/gmap/Makefile (revision 460451) +++ head/biology/gmap/Makefile (revision 460452) @@ -1,40 +1,40 @@ # Created by: Bob Zimmermann # $FreeBSD$ PORTNAME= gmap PORTVERSION= 2015.09.21 CATEGORIES= biology MASTER_SITES= http://research-pub.gene.com/gmap/src/ DISTNAME= ${PORTNAME}-gsnap-${PORTVERSION:C|\.|-|g} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Genomic Mapping and Alignment Program for mRNA and EST Sequences LICENSE= GMAP LICENSE_NAME= GMAP License LICENSE_FILE= ${WRKSRC}/COPYING LICENSE_PERMS= dist-mirror pkg-mirror auto-accept BROKEN_aarch64= invokes x86 assembler BROKEN_armv6= invokes x86 assembler BROKEN_armv7= invokes x86 assembler BROKEN_mips64= invokes x86 assembler BROKEN_powerpc64= invokes x86 assembler BROKEN_sparc64= invokes x86 assembler USES= gmake perl5 GNU_CONFIGURE= yes WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION:C|\.|-|g} OPTIONS_DEFINE= SIMD SIMD_CONFIGURE_OFF= --disable-builtin-popcount --disable-simd # shebang_fix operates during patch. # These scripts are created during configure. post-configure: ${REINPLACE_CMD} -e 's|/usr/bin/perl|${PERL}|g' \ ${WRKSRC}/Makefile ${WRKSRC}/util/*.pl .include Index: head/biology/jellyfish/Makefile =================================================================== --- head/biology/jellyfish/Makefile (revision 460451) +++ head/biology/jellyfish/Makefile (revision 460452) @@ -1,40 +1,39 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= jellyfish PORTVERSION= 2.2.6 PORTREVISION= 2 DISTVERSIONPREFIX= v CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Fast, memory-efficient counting of k-mers in DNA LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE BUILD_DEPENDS= yaggo:devel/yaggo GNU_CONFIGURE= yes USES= autoreconf compiler:c++11-lib gmake libtool pathfix pkgconfig USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= gmarcais GH_PROJECT= Jellyfish INSTALL_TARGET= install-strip PLIST_SUB= VER=${PORTVERSION} BROKEN_aarch64= Fails to compile: error: variable res is uninitialized .include # SSE code assumes amd64 features .if ${ARCH} != "amd64" CONFIGURE_ARGS+=--without-sse .endif .include Index: head/biology/libgtextutils/Makefile =================================================================== --- head/biology/libgtextutils/Makefile (revision 460451) +++ head/biology/libgtextutils/Makefile (revision 460452) @@ -1,22 +1,21 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= libgtextutils PORTVERSION= 0.7 CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Gordon's text utilities LICENSE= AGPLv3 USES= autoreconf libtool pathfix pkgconfig GNU_CONFIGURE= yes USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= agordon INSTALL_TARGET= install-strip .include Index: head/biology/ncbi-blast+/Makefile =================================================================== --- head/biology/ncbi-blast+/Makefile (revision 460451) +++ head/biology/ncbi-blast+/Makefile (revision 460452) @@ -1,58 +1,57 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= blast+ PORTVERSION= 2.5.0 PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PORTVERSION}/ \ http://acadix.biz/Ports/distfiles/ PKGNAMEPREFIX= ncbi- DISTNAME= ncbi-blast-${PORTVERSION}+-src -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= NCBI implementation of Basic Local Alignment Search Tool LICENSE= PD LICENSE_FILE= ${WRKSRC}/scripts/projects/blast/LICENSE LIB_DEPENDS= libpcre.so:devel/pcre RUN_DEPENDS= p5-List-MoreUtils>=0:lang/p5-List-MoreUtils WRKSRC= ${WRKDIR}/${DISTNAME}/c++ GNU_CONFIGURE= yes USES= gmake shebangfix perl5 python SHEBANG_FILES= src/app/blast/legacy_blast.pl \ src/app/blast/update_blastdb.pl \ src/app/winmasker/windowmasker_2.2.22_adapter.py MAKE_JOBS_UNSAFE= yes # Requires openmp USE_GCC= yes USE_LDCONFIG= yes # The test for amq can hang, but amq is not needed so just avoid the test CONFIGURE_ENV= ncbi_cv_prog_amq_w=no # configure chooses /usr/local/bin/ar with no flags # FreeBSD boost port flagged by configure as untested version CONFIGURE_ARGS+=AR="ar cr" --without-boost # Fix "undefined _ThreadRuneLocale" error on 10.0 # Fix unknown options in configure # Add staging support to configure-generated Makefile post-patch: ${REINPLACE_CMD} \ -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' \ -e '/--infodir=DIR/d' \ -e '/--mandir=DIR/d' \ ${WRKSRC}/src/build-system/configure ${REINPLACE_CMD} -e 's|@prefix@|${STAGEDIR}@prefix@|g' \ ${WRKSRC}/src/build-system/Makefile.in.top post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/*.so .include Index: head/biology/p5-transdecoder/Makefile =================================================================== --- head/biology/p5-transdecoder/Makefile (revision 460451) +++ head/biology/p5-transdecoder/Makefile (revision 460452) @@ -1,45 +1,44 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= transdecoder PORTVERSION= 2.1.0 DISTVERSIONPREFIX=v CATEGORIES= biology perl5 PKGNAMEPREFIX= p5- -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Identify candidate coding regions within transcript sequences LICENSE= BSD3CLAUSE RUN_DEPENDS= cd-hit>=4.6.1:biology/cd-hit \ p5-URI>0:net/p5-URI NO_BUILD= yes NO_ARCH= yes USES= perl5 shebangfix SHEBANG_FILES= sample_data/cufflinks_example/runMe.sh \ sample_data/pasa_example/runMe.sh \ sample_data/simple_transcriptome_target/runMe.sh \ util/pfam_mpi.pbs USE_GITHUB= yes GH_PROJECT= TransDecoder PERL_MOD_DIR= ${PREFIX}/${SITE_PERL_REL}/${PORTNAME} PERL_UTIL_DIR= ${PREFIX}/libexec/${PORTNAME} post-patch: ${REINPLACE_CMD} \ -e 's|$$FindBin::RealBin/PerlLib|${PERL_MOD_DIR}|g' \ -e 's|$$FindBin::Bin/../PerlLib|${PERL_MOD_DIR}|g' \ -e 's|$$FindBin::RealBin/util|${PERL_UTIL_DIR}|g' \ ${WRKSRC}/TransDecoder* ${WRKSRC}/util/*.pl do-install: ${MKDIR} ${STAGEDIR}${PERL_MOD_DIR} ${STAGEDIR}${PERL_UTIL_DIR} ${INSTALL_SCRIPT} ${WRKSRC}/PerlLib/* ${STAGEDIR}${PERL_MOD_DIR} ${INSTALL_SCRIPT} ${WRKSRC}/TransDecoder* ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${WRKSRC}/util/*.pl ${STAGEDIR}${PERL_UTIL_DIR} .include Index: head/biology/plink/Makefile =================================================================== --- head/biology/plink/Makefile (revision 460451) +++ head/biology/plink/Makefile (revision 460452) @@ -1,29 +1,28 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= plink PORTVERSION= 1.07 PORTREVISION= 7 CATEGORIES= biology science MASTER_SITES= http://pngu.mgh.harvard.edu/~purcell/plink/dist/ DISTNAME= ${PORTNAME}-${PORTVERSION}-src -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Whole genome association analysis toolset BROKEN= no public distfiles LICENSE= GPLv2 LIB_DEPENDS= liblapack.so:math/lapack # We need Fortran LDFLAGS to link with Lapack. USES= fortran gmake zip PLIST_FILES= bin/plink do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/plink ${STAGEDIR}${PREFIX}/bin .include Index: head/biology/plinkseq/Makefile =================================================================== --- head/biology/plinkseq/Makefile (revision 460451) +++ head/biology/plinkseq/Makefile (revision 460452) @@ -1,45 +1,44 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= plinkseq PORTVERSION= 0.10 PORTREVISION= 1 CATEGORIES= biology science MASTER_SITES= http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/ # Default DISTNAME is correct, so leave it alone. DISTFILES= ${PORTNAME}-src-${PORTVERSION}.tgz -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Toolset for working with human genetic variation data LICENSE= GPLv2 BROKEN_aarch64= Does not build: Host architecture was not detected as supported by protobuf BROKEN_mips64= Does not build: Host architecture was not detected as supported by protobuf BROKEN_powerpc64= Does not build: atomicops.h: error: stray '\#' in program USES= libtool gmake post-patch: ${REINPLACE_CMD} \ -e 's|PF_INET|AF_INET|g' \ ${WRKSRC}/sources/mongoose/sources/lib/mongoose.c ${REINPLACE_CMD} \ -e 's|g++|${CXX}|g' \ -e 's|gcc|${CC}|g' \ -e 's|CXXFLAGS = -O3|CXXFLAGS = ${CXXFLAGS}|g' \ -e 's|ALL_CFLAGS =-O3|ALL_CFLAGS = ${CFLAGS}|g' \ ${WRKSRC}/config_defs.Makefile ${REINPLACE_CMD} \ -e 's| -ldl||g' \ -e 's| $$(STATIC_FLAG)||g' \ ${WRKSRC}/Makefile do-install: .for f in behead browser gcol mm mongoose pdas pseq smp tab2vcf ${INSTALL_PROGRAM} ${WRKSRC}/build/execs/${f} ${STAGEDIR}${PREFIX}/bin .endfor ${INSTALL_DATA} ${WRKSRC}/sources/plinkseq/build/lib/libplinkseq.a \ ${STAGEDIR}${PREFIX}/lib .include Index: head/biology/slclust/Makefile =================================================================== --- head/biology/slclust/Makefile (revision 460451) +++ head/biology/slclust/Makefile (revision 460452) @@ -1,22 +1,21 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= slclust PORTVERSION= 2010.02.02 CATEGORIES= biology MASTER_SITES= SF/slclust/slclust DISTNAME= ${PORTNAME}_02022010 -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Single-linkage clustering with Jaccard similarity LICENSE= ART10 WRKSRC= ${WRKDIR}/${PORTNAME} PLIST_FILES= bin/slclust do-install: ${INSTALL_PROGRAM} ${WRKSRC}/src/slclust ${STAGEDIR}${PREFIX}/bin .include Index: head/biology/trimmomatic/Makefile =================================================================== --- head/biology/trimmomatic/Makefile (revision 460451) +++ head/biology/trimmomatic/Makefile (revision 460452) @@ -1,27 +1,27 @@ # Created by: Dan Siercks # $FreeBSD$ PORTNAME= trimmomatic PORTVERSION= 0.35 CATEGORIES= biology java MASTER_SITES= http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/ DISTNAME= Trimmomatic-${PORTVERSION} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Flexible read trimming tool for Illumina NGS data LICENSE= GPLv3 USES= zip USE_JAVA= yes JAVA_VERSION= 1.6+ JAVA_RUN= yes NO_BUILD= yes NO_ARCH= yes do-install: ${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PORTVERSION}.jar \ ${STAGEDIR}${JAVAJARDIR}/trimmomatic.jar cd ${WRKSRC} && ${COPYTREE_SHARE} adapters ${STAGEDIR}${DATADIR} .include Index: head/biology/vcftools/Makefile =================================================================== --- head/biology/vcftools/Makefile (revision 460451) +++ head/biology/vcftools/Makefile (revision 460452) @@ -1,19 +1,18 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= vcftools PORTVERSION= 0.1.15 DISTVERSIONPREFIX= v CATEGORIES= biology -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for working with VCF genomics files LICENSE= LGPL3 USES= autoreconf gmake perl5 pkgconfig GNU_CONFIGURE= yes USE_GITHUB= yes .include Index: head/comms/cutecom/Makefile =================================================================== --- head/comms/cutecom/Makefile (revision 460451) +++ head/comms/cutecom/Makefile (revision 460452) @@ -1,18 +1,18 @@ # Created by: Markus Brueffer # $FreeBSD$ PORTNAME= cutecom PORTVERSION= 0.20.0 PORTREVISION= 2 CATEGORIES= comms MASTER_SITES= http://cutecom.sourceforge.net/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Graphical serial terminal RUN_DEPENDS= lsz:comms/lrzsz USE_QT4= qt3support qmake_build moc_build rcc_build uic_build USES= cmake .include Index: head/devel/libgamepad/Makefile =================================================================== --- head/devel/libgamepad/Makefile (revision 460451) +++ head/devel/libgamepad/Makefile (revision 460452) @@ -1,22 +1,21 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= libgamepad PORTVERSION= 0.1.2 CATEGORIES= devel games MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Generic gamepad API LICENSE= BSD2CLAUSE USES= tar:xz pre-build: (cd ${WRKSRC} && make depend) MAKE_FLAGS+= PREFIX=${STAGEDIR}${PREFIX} \ MANPREFIX=${STAGEDIR}${PREFIX} .include Index: head/devel/libnxt/Makefile =================================================================== --- head/devel/libnxt/Makefile (revision 460451) +++ head/devel/libnxt/Makefile (revision 460452) @@ -1,27 +1,26 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= libnxt PORTVERSION= 0.3 CATEGORIES= devel MASTER_SITES= https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/libnxt/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Lego NXT library SUB_FILES= pkg-message USES= python:2.7,build scons shebangfix USE_LDCONFIG= yes SHEBANG_FILES= make_flash_header.py do-install: @${MKDIR} ${STAGEDIR}${PREFIX}/include/libnxt ${INSTALL_PROGRAM} ${WRKSRC}/fwflash ${STAGEDIR}${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/fwexec ${STAGEDIR}${PREFIX}/bin ${INSTALL_DATA} ${WRKSRC}/libnxt.a ${STAGEDIR}${PREFIX}/lib @${MKDIR} ${STAGEDIR}${PREFIX}/include/libnxt .for file in ${WRKSRC}/*.h ${INSTALL_DATA} ${WRKSRC}/${file} ${STAGEDIR}${PREFIX}/include/libnxt .endfor .include Index: head/devel/libsysinfo/Makefile =================================================================== --- head/devel/libsysinfo/Makefile (revision 460451) +++ head/devel/libsysinfo/Makefile (revision 460452) @@ -1,29 +1,28 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= libsysinfo PORTVERSION= 0.0.3 DISTVERSIONPREFIX= v PORTREVISION= 1 CATEGORIES= devel MAINTAINER= imp@bsdimp.com COMMENT= GNU libc's sysinfo port for FreeBSD LICENSE= BSD3CLAUSE USE_GITHUB= yes GH_ACCOUNT= bsdimp USES= uidfix USE_LDCONFIG= yes LDFLAGS+= -lkvm PLIST_FILES= include/sys/sysinfo.h \ lib/libsysinfo.a \ lib/libsysinfo.so \ lib/libsysinfo.so.0 \ man/man3/sysinfo.3.gz .include Index: head/devel/lnphost/Makefile =================================================================== --- head/devel/lnphost/Makefile (revision 460451) +++ head/devel/lnphost/Makefile (revision 460452) @@ -1,29 +1,28 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= lnphost PORTVERSION= 1.0a CATEGORIES= devel MASTER_SITES= SF -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Lego RCX iinfrared communication API LICENSE= GPLv2 USES= zip gmake WRKSRC= ${WRKDIR}/lnphost CFLAGS+= -DHAVE_STRING_H PLIST_FILES= bin/lnpdump \ lib/lnphost.a \ include/lnphost.h \ man/man1/lnpdump.1.gz MAKE_ARGS= PREFIX=${STAGEDIR}${PREFIX} # Use system getopt post-patch: ${RM} ${WRKSRC}/Include/getopt.h ${WRKSRC}/Modules/getopt.c .include Index: head/devel/p5-Device-USB/Makefile =================================================================== --- head/devel/p5-Device-USB/Makefile (revision 460451) +++ head/devel/p5-Device-USB/Makefile (revision 460452) @@ -1,29 +1,28 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= Device-USB PORTVERSION= 0.35 PORTREVISION= 2 CATEGORIES= devel perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= josh.carroll@gmail.com COMMENT= Perl wrapper for libusb LICENSE= ART10 GPLv1+ LICENSE_COMB= dual BUILD_DEPENDS= p5-Inline>=0:devel/p5-Inline \ p5-Inline-C>=0:devel/p5-Inline-C RUN_DEPENDS:= ${BUILD_DEPENDS} MAKE_JOBS_UNSAFE=yes USES= perl5 USE_PERL5= configure post-patch: @${REINPLACE_CMD} -e 's|dump_usb.pl|lib/Device/&|' ${WRKSRC}/MANIFEST @${MV} ${WRKSRC}/dump_usb.pl ${WRKSRC}/lib/Device/ .include Index: head/devel/py-instant/Makefile =================================================================== --- head/devel/py-instant/Makefile (revision 460451) +++ head/devel/py-instant/Makefile (revision 460452) @@ -1,29 +1,29 @@ # Created by: Li-Wen Hsu # $FreeBSD$ PORTNAME= instant PORTVERSION= ${MMVERSION}.0 PORTREVISION= 1 CATEGORIES= devel python MASTER_SITES= https://launchpad.net/${PORTNAME}/${MMVERSION}.x/${PORTVERSION}/+download/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Python module for instant inlining of C and C++ code in Python LICENSE= LGPL3 RUN_DEPENDS= swig3.0:devel/swig30 USES= python:2 USE_PYTHON= distutils PYDISTUTILS_PKGNAME= instant MMVERSION= 1.2 post-patch: @${REINPLACE_CMD} -e \ 's|\[(join("share", "man", "man1"),|\[(join("man", "man1"),|' \ ${WRKSRC}/setup.py .include Index: head/devel/roboctl/Makefile =================================================================== --- head/devel/roboctl/Makefile (revision 460451) +++ head/devel/roboctl/Makefile (revision 460452) @@ -1,37 +1,36 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= roboctl PORTVERSION= 0.3.8 CATEGORIES= devel MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= API and tools for communicating with Lego and Vex robots LICENSE= GPLv3 BUILD_DEPENDS= ${LOCALBASE}/lib/libgamepad.a:devel/libgamepad MAKE_ENV= EXTRALIBS=-lbluetooth MAKE_FLAGS+= PREFIX=${STAGEDIR}${PREFIX} \ MANPREFIX=${STAGEDIR}${PREFIX} MAKE_JOBS_UNSAFE= yes USES= tar:xz OPTIONS_DEFINE= CUTECOM CUTECOM_DESC= Install cutecom for Vex debugging CUTECOM_RUN_DEPENDS= cutecom:comms/cutecom pre-build: (cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} ${MAKE} depend) post-install: (cd ${WRKSRC}/Commands/NXTRemote; ${MAKE}) ${INSTALL_PROGRAM} ${WRKSRC}/Commands/NXTRemote/nxtremote ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${WRKSRC}/Scripts/lego_bluetooth_config ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/Commands/NXTRemote/nxtremote.1 ${STAGEDIR}${MANPREFIX}/man/man1 .include Index: head/devel/yaggo/Makefile =================================================================== --- head/devel/yaggo/Makefile (revision 460451) +++ head/devel/yaggo/Makefile (revision 460452) @@ -1,22 +1,21 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= yaggo PORTVERSION= 1.5.9 DISTVERSIONPREFIX= v CATEGORIES= devel -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Generate command line parser using getopt_long LICENSE= GPLv3 NO_ARCH= yes USE_RUBY= yes USE_GITHUB= yes GH_ACCOUNT= gmarcais PLIST_FILES= bin/yaggo man/man1/yaggo.1.gz share/doc/yaggo/README.md .include Index: head/lang/nbc/Makefile =================================================================== --- head/lang/nbc/Makefile (revision 460451) +++ head/lang/nbc/Makefile (revision 460452) @@ -1,49 +1,47 @@ # Created by: Ivan "Rambius" Ivanov # $FreeBSD$ -# Also created by: Jason Bacon - PORTNAME= nbc PORTVERSION= 1.2.1.r4 PORTREVISION= 10 CATEGORIES= lang MASTER_SITES= SF/bricxcc/NBC_NXC/NBC%20release%20${PORTVERSION:S/.r/%20r/} DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= rene@FreeBSD.org COMMENT= Programming language for the LEGO MINDSTORMS NXT MAKE_JOBS_UNSAFE= yes MAKEFILE= nbcunix.mak WRKSRC= ${WRKDIR}/NXT OPTIONS_DEFINE= DOCS ROBOCTL ROBOCTL_DESC= Include roboctl to communicate with the NXT ROBOCTL_RUN_DEPENDS= legoctl:devel/roboctl USES= dos2unix gmake tar:tgz USE_FPC= fcl-base fcl-image pasjpeg rtl-objpas PLIST_FILES= bin/nbc \ include/nbc/NXCDefs.h \ include/nbc/NBCCommon.h \ include/nbc/NXTDefs.h PORTDOCS= Changelog \ Readme post-patch: @${REINPLACE_CMD} -e 's|/usr/local|${LOCALBASE}|' ${WRKSRC}/${MAKEFILE} @${REINPLACE_CMD} -e 's|/usr/bin|${LOCALBASE}/bin|' ${WRKSRC}/${MAKEFILE} do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/include/nbc ${INSTALL_PROGRAM} ${WRKSRC}/nbc ${STAGEDIR}${PREFIX}/bin ${INSTALL_DATA} ${WRKSRC}/*.h ${STAGEDIR}${PREFIX}/include/nbc ${MKDIR} ${STAGEDIR}${DOCSDIR} .for f in ${PORTDOCS} ${INSTALL_DATA} ${WRKDIR}/doc/${f} ${STAGEDIR}${DOCSDIR} .endfor .include Index: head/lang/x10/Makefile =================================================================== --- head/lang/x10/Makefile (revision 460451) +++ head/lang/x10/Makefile (revision 460452) @@ -1,77 +1,76 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= x10 PORTVERSION= 2.2.1 PORTREVISION= 6 CATEGORIES= lang devel java MASTER_SITES= http://dist.codehaus.org/x10/dependencies/ \ SF DISTNAME= ${PORTNAME}-${PORTVERSION}-src DISTFILES= ${DISTNAME}${EXTRACT_SUFX} \ lpg.runtime.java_2.0.22.jar \ ecj-3.5.1.jar \ com.ibm.wala.cast.java_1.0.0.201101071300.jar \ com.ibm.wala.cast_1.0.0.201101071300.jar \ com.ibm.wala.core_1.1.3.201101071300.jar \ com.ibm.wala.shrike_1.3.1.201101071300.jar \ org.eclipse.equinox.common_3.6.0.v20100503.jar \ commons-math-2.2.jar \ bdwgc-7.1.tar.gz EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Object-oriented parallel programming language LICENSE= EPL BROKEN= Fails to build with modern compilers (cf. PR 219282) USES= tar:bzip2 USE_JAVA= yes JAVA_VERSION= 1.6 1.7 USE_ANT= yes USE_GCC= yes USE_LDCONFIG= ${PREFIX}/stdlib/lib # Can't have USE_GMAKE with USE_ANT: They imply conflicting do-build actions. BUILD_DEPENDS+= gmake:devel/gmake \ bash:shells/bash WRKSRC= ${WRKDIR}/x10.dist OPTIONS_DEFINE= EXAMPLES .include post-patch: ${REINPLACE_CMD} -e 's/value="make"/value="gmake"/g' \ ${WRKDIR}/x10.runtime/build.xml ${MKDIR} ${WRKSRC}/lib ${WRKDIR}/x10.runtime/src-cpp/bdwgc/src ${CP} ${DISTDIR}/lpg.runtime.java_2.0.22.jar ${WRKSRC}/lib/lpg.jar ${CP} ${DISTDIR}/ecj-3.5.1.jar ${WRKSRC}/lib/ecj.jar ${CP} ${DISTDIR}/com.ibm.wala.cast.java_1.0.0.201101071300.jar ${WRKSRC}/lib ${CP} ${DISTDIR}/com.ibm.wala.cast_1.0.0.201101071300.jar ${WRKSRC}/lib ${CP} ${DISTDIR}/com.ibm.wala.core_1.1.3.201101071300.jar ${WRKSRC}/lib ${CP} ${DISTDIR}/com.ibm.wala.shrike_1.3.1.201101071300.jar ${WRKSRC}/lib ${CP} ${DISTDIR}/org.eclipse.equinox.common_3.6.0.v20100503.jar ${WRKSRC}/lib ${CP} ${DISTDIR}/commons-math-2.2.jar ${WRKSRC}/lib ${CP} ${DISTDIR}/bdwgc-7.1.tar.gz ${WRKDIR}/x10.runtime/src-cpp/bdwgc (cd ${WRKDIR}/x10.runtime/src-cpp/bdwgc/src && tar zxvf ../bdwgc-7.1.tar.gz && ${REINPLACE_CMD} -e 's|freebsd1\*|freebsd1.*|g' configure) do-install: .for f in X10Launcher apgas precommit x10 x10c x10c++ x10j ${INSTALL_SCRIPT} ${WRKSRC}/bin/${f} ${STAGEDIR}${PREFIX}/bin .endfor ${MKDIR} ${STAGEDIR}${PREFIX}/stdlib ${INSTALL_DATA} ${WRKSRC}/etc/* ${STAGEDIR}${PREFIX}/etc ${INSTALL_DATA} ${WRKSRC}/include/* ${STAGEDIR}${PREFIX}/include ${INSTALL_DATA} ${WRKSRC}/lib/* ${STAGEDIR}${PREFIX}/lib ${CP} -R ${WRKSRC}/stdlib/* ${STAGEDIR}${PREFIX}/stdlib .if ${PORT_OPTIONS:MEXAMPLES} ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${CP} -R ${WRKSRC}/samples/* ${STAGEDIR}${EXAMPLESDIR} .endif .include Index: head/math/matlab-installer/Makefile =================================================================== --- head/math/matlab-installer/Makefile (revision 460451) +++ head/math/matlab-installer/Makefile (revision 460452) @@ -1,33 +1,32 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= matlab-installer PORTVERSION= 0.2 PORTREVISION= 4 CATEGORIES= math science java MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Easy installation of Linux Matlab(r) on FreeBSD LICENSE= BSD3CLAUSE RUN_DEPENDS= mount_cd9660_image:sysutils/diskimage-tools \ auto-ask:sysutils/auto-admin \ webbrowser:www/webbrowser \ USES= linux tar:xz USE_LINUX= dri devtools USE_JAVA= yes JAVA_VERSION= 1.6+ JAVA_OS= linux JAVA_RUN= yes NO_BUILD= yes PLIST_FILES= bin/${PORTNAME} man/man1/${PORTNAME}.1.gz do-install: ${INSTALL_SCRIPT} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/matlab-installer.1 ${STAGEDIR}${PREFIX}/man/man1 .include Index: head/math/py-ffc/Makefile =================================================================== --- head/math/py-ffc/Makefile (revision 460451) +++ head/math/py-ffc/Makefile (revision 460452) @@ -1,25 +1,24 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= ffc PORTVERSION= ${MMVERSION}.0 CATEGORIES= math python MASTER_SITES= https://launchpad.net/${PORTNAME}/${MMVERSION}.x/${PORTVERSION}/+download/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= C++ code generator for multilinear forms LICENSE= LGPL3 USES= python:2 USE_PYTHON= distutils PYDISTUTILS_PKGNAME= FFC MMVERSION= 1.2 post-patch: ${REINPLACE_CMD} -i '' -e 's|os.path.join(os.path.sep, "usr")|os.path.normpath("${PREFIX}")|' \ ${WRKSRC}/test/regression/test.py .include Index: head/math/py-fiat/Makefile =================================================================== --- head/math/py-fiat/Makefile (revision 460451) +++ head/math/py-fiat/Makefile (revision 460452) @@ -1,25 +1,24 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= fiat PORTVERSION= ${MMVERSION}.0 PORTREVISION= 3 CATEGORIES= math python MASTER_SITES= https://launchpad.net/${PORTNAME}/${MMVERSION}.x/release-${MMVERSION}/+download/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME}-${MMVERSION} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= FInite element Automatic Tabulator LICENSE= LGPL3 BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}scientific>=0:math/py-scientific@${FLAVOR} RUN_DEPENDS:= ${BUILD_DEPENDS} USES= python:2 USE_PYTHON= distutils autoplist MMVERSION= 1.1 .include Index: head/math/py-ufl/Makefile =================================================================== --- head/math/py-ufl/Makefile (revision 460451) +++ head/math/py-ufl/Makefile (revision 460452) @@ -1,25 +1,24 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= ufl PORTVERSION= ${MMVERSION}0 CATEGORIES= math python MASTER_SITES= https://launchpad.net/${PORTNAME}/${MMVERSION}.x/${MMVERSION}.0/+download/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= ${PORTNAME}-${MMVERSION}.0 -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Unified Form Language for finite element discretizations LICENSE= LGPL3 USES= python:2 USE_PYTHON= distutils autoplist MMVERSION= 1.2 post-patch: @${REINPLACE_CMD} -e 's|\[(pjoin("share", "man", "man1"),|\[(pjoin("man", "man1"),|' \ ${WRKSRC}/setup.py .include Index: head/math/py-viper/Makefile =================================================================== --- head/math/py-viper/Makefile (revision 460451) +++ head/math/py-viper/Makefile (revision 460452) @@ -1,22 +1,21 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= viper PORTVERSION= 1.0.1 CATEGORIES= math python MASTER_SITES= https://launchpad.net/fenics-${PORTNAME}/${MMVERSION}.x/${PORTVERSION}/+download/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Minimalistic scientific plotter and visualization module LICENSE= LGPL3 USES= python:2 USE_PYTHON= distutils autoplist post-patch: @${REINPLACE_CMD} -e 's|data_files=\[(join("share", "man", "man1"),|data_files=\[(join("man", "man1"),|' \ ${WRKSRC}/setup.py .include Index: head/math/rapid/Makefile =================================================================== --- head/math/rapid/Makefile (revision 460451) +++ head/math/rapid/Makefile (revision 460452) @@ -1,35 +1,34 @@ -# Created by: Jason W. Bacon # $FreeBSD$ PORTNAME= rapid PORTVERSION= 2.01 CATEGORIES= math science graphics MASTER_SITES= http://www.cs.sunysb.edu/~algorith/implement/RAPID/distrib/ \ http://www.neuro.mcw.edu/Ports/distfiles/ DISTNAME= RAPID_v2_01 -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Robust and Accurate Polygon Interference Detection RESTRICTED= For any commercial purpose, you must request a license from http://www.cs.unc.edu/~geom/OBB/OBBT.html SUB_FILES= pkg-message PKGMESSAGE= ${WRKDIR}/pkg-message ALL_TARGET= MAKE_JOBS_UNSAFE= yes MAKE_ENV+= V=1 .include post-extract: ${REINPLACE_CMD} -E "s/friend RAPID_Collide/friend int RAPID_Collide/" ${WRKSRC}/RAPID_private.H do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/include/RAPID ${INSTALL_DATA} ${WRKSRC}/*.H ${STAGEDIR}${PREFIX}/include/RAPID ${INSTALL_DATA} ${WRKSRC}/libRAPID.a ${STAGEDIR}${PREFIX}/lib ${INSTALL_MAN} ${FILESDIR}/rapid.1 ${STAGEDIR}${MANPREFIX}/man/man1 .include Index: head/math/ufc/Makefile =================================================================== --- head/math/ufc/Makefile (revision 460451) +++ head/math/ufc/Makefile (revision 460452) @@ -1,27 +1,26 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= ufc PORTVERSION= ${MMVERSION}.0 PORTREVISION= 7 CATEGORIES= math python MASTER_SITES= http://launchpad.net/${PORTNAME}/${MMVERSION}.x/${PORTVERSION}/+download/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Unified framework for finite element assembly BUILD_DEPENDS= swig3.0:devel/swig30 LIB_DEPENDS= libboost_math_c99.so:devel/boost-libs # LICENSE= public domain USES= cmake python:2 CMAKE_ARGS+= -DUFC_PKGCONFIG_DIR=${PREFIX}/libdata/pkgconfig MMVERSION= 2.2 post-patch: ${REINPLACE_CMD} -i '' -e 's|os.path.join(os.path.sep, "usr")|os.path.normpath("${PREFIX}")|' ${WRKSRC}/src/utils/python/ufc_utils/build.py .include Index: head/multimedia/vtkmpeg2encode/Makefile =================================================================== --- head/multimedia/vtkmpeg2encode/Makefile (revision 460451) +++ head/multimedia/vtkmpeg2encode/Makefile (revision 460452) @@ -1,60 +1,59 @@ -# Created by: Jason W. Bacon # $FreeBSD$ PORTNAME= vtkmpeg2encode PORTVERSION= ${VTK_VERSION} PORTREVISION= 1 CATEGORIES= multimedia math MASTER_SITES= http://www.vtk.org/files/support/ \ http://www.neuro.mcw.edu/Ports/distfiles/VTK5/ DISTNAME= vtkmpeg2encode MAINTAINER= ports@FreeBSD.org COMMENT= VTK MPEG2 encoding library LICENSE= MPEG-2 LICENSE_NAME= MPEG-2 license LICENSE_FILE= ${WRKSRC}/mpeg2enc.h LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept USES= cmake USE_LDCONFIG= yes CMAKE_ARGS?= -DBUILD_SHARED_LIBS:BOOL=ON VTK_VERSION= 5.10.1 SUB_FILES= vtkmpeg2encode.3 MPEGLIB= libvtkMPEG2Encode PLIST_FILES= lib/${MPEGLIB}.so.${PORTVERSION} \ lib/${MPEGLIB}.so.${VTK_VERSION:R} \ lib/${MPEGLIB}.so.${VTK_VERSION:R:R} \ lib/${MPEGLIB}.so \ include/vtk-${VTK_VERSION:R}/mpeg2encDllConfig.h \ include/vtk-${VTK_VERSION:R}/mpeg2enc_global.h \ include/vtk-${VTK_VERSION:R}/mpeg2enc.h \ include/vtk-${VTK_VERSION:R}/mpeg2enc_config.h \ include/vtk-${VTK_VERSION:R}/vlc.h \ man/man3/vtkmpeg2encode.3.gz post-build: ${MV} ${WRKSRC}/${MPEGLIB}.so ${WRKSRC}/${MPEGLIB}.so.${PORTVERSION} do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/include/vtk-${VTK_VERSION:R} ${INSTALL_LIB} ${WRKSRC}/${MPEGLIB}.so.${PORTVERSION} ${STAGEDIR}${PREFIX}/lib ${LN} -s ${MPEGLIB}.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/${MPEGLIB}.so.${VTK_VERSION:R} ${LN} -s ${MPEGLIB}.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/${MPEGLIB}.so.${VTK_VERSION:R:R} ${LN} -s ${MPEGLIB}.so.${PORTVERSION} \ ${STAGEDIR}${PREFIX}/lib/${MPEGLIB}.so ${INSTALL_DATA} ${WRKSRC}/mpeg2encDllConfig.h \ ${WRKSRC}/mpeg2enc_global.h \ ${WRKSRC}/mpeg2enc.h \ ${WRKSRC}/mpeg2enc_config.h \ ${WRKSRC}/vlc.h \ ${STAGEDIR}${PREFIX}/include/vtk-${VTK_VERSION:R} ${INSTALL_MAN} ${WRKDIR}/vtkmpeg2encode.3 ${STAGEDIR}${MANPREFIX}/man/man3 .include Index: head/ports-mgmt/genplist/Makefile =================================================================== --- head/ports-mgmt/genplist/Makefile (revision 460451) +++ head/ports-mgmt/genplist/Makefile (revision 460452) @@ -1,23 +1,22 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= genplist PORTVERSION= 1.2 CATEGORIES= ports-mgmt MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Generates a static plist for a port LICENSE= BSD2CLAUSE NO_BUILD= yes USES= tar:xz PLIST_FILES= bin/genplist man/man1/genplist.1.gz do-install: ${INSTALL_SCRIPT} ${WRKSRC}/genplist ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/genplist.1 ${STAGEDIR}${PREFIX}/man/man1 .include Index: head/science/afni/Makefile =================================================================== --- head/science/afni/Makefile (revision 460451) +++ head/science/afni/Makefile (revision 460452) @@ -1,162 +1,161 @@ -# Created by: Jason W. Bacon # $FreeBSD$ ############################################################################ # http://www.neuro.mcw.edu/Ports has the latest source distribution from # which this port is built. It will be updated as time permits. # # afni.nimh.nih.gov is the ultimate source for AFNI, and will always # contain the latest source release. If this port is not up to date, # you can download the latest sources and build manually. PORTNAME= afni PORTVERSION= 2015.11.13 PORTREVISION= 5 CATEGORIES= science biology graphics MASTER_SITES= http://www.acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Advanced Functional Neuro Imaging LICENSE= GPLv2 BUILD_DEPENDS= gm4:devel/m4 LIB_DEPENDS= libexpat.so:textproc/expat2 \ libf2c.so:lang/f2c \ libR.so:math/R \ libgsl.so:math/gsl \ libnetcdff.so:science/netcdf-fortran \ libxml2.so:textproc/libxml2 \ libXm.so:x11-toolkits/open-motif RUN_DEPENDS= endian:sysutils/endian \ mpeg_encode:multimedia/mpeg_encode \ ppmtogif:graphics/netpbm \ qhull:math/qhull5 BROKEN_aarch64= fails to compile: suma_utils.c:3043:10: statement requires expression of scalar type BROKEN_sparc64= fails to compile: undefined reference to '_mcount' CONFLICTS= im-[0-9]* \ nifticlib-[0-9]* \ open-usp-tukubai-[0-9]* USES= gettext gmake iconv jpeg:run motif perl5 python shebangfix tar:xz SHEBANG_FILES= suma_change_spec \ 3dPAR2AFNI.pl \ python_scripts/*.py \ pkundu/meica.py \ pkundu/meica.libs/*.py \ pkundu/meica.libs/mdp/test/run_tests.py USE_GNOME= glib20 .include USE_GL= gl glu glw USE_XORG= x11 xext xi xmu xp xt MAKE_ENV= CC="${CC}" R_SHARE_DIR=${LOCALBASE}/lib/R/share MAKE_JOBS_UNSAFE=yes ALL_TARGET= vastness suma ########################################################################### # Install parameters SUB_FILES= pkg-message afni.cshrc afni.profile INSTALL_WRKSRC= ${WRKSRC}/BSD PRESTAGE= ${WRKSRC}/prestage X11R6_FILES= coxplot/Makefile \ coxplot/Makefile.f2c \ 3DEdge/src/Makefile \ SUMA/SUMA_Makefile \ edt_blur.c \ suma_datasets.c \ SUMA/SUMA_Load_Surface_Object.c \ SUMA/SUMA_MiscFunc.c \ SUMA/SUMA_ParseCommands.c \ SUMA/GLUT/libglut/glut_event.c \ SUMA/SUMA_Surface_IO.c post-extract: .for f in ${X11R6_FILES} @${REINPLACE_CMD} \ -e 's|/usr/X11R6|$${LOCALBASE}|g' ${WRKSRC}/${f} .endfor @${REINPLACE_CMD} \ -E 's|AFNI_[0-9_]+|${PORTVERSION}|g' ${WRKSRC}/AFNI_label.h @${REINPLACE_CMD} \ -e "s|%%PREFIX%%|${PREFIX}|g" ${WRKSRC}/afni.1 @${CP} ${FILESDIR}/Makefile ${WRKSRC} @${RM} ${WRKSRC}/3DEdge/src/Makefile.orig # shebangfix misses /bin/python on 10.1 post-patch: ${REINPLACE_CMD} -e "s|-lglib|-lglib-2.0|g" \ ${WRKSRC}/SUMA/SUMA_Makefile ${REINPLACE_CMD} -e "s|/bin/python|${PYTHON_CMD}|g" \ ${WRKSRC}/python_scripts/lib_fat_Rfactor.py ${REINPLACE_CMD} \ -e 's|os\.path\.dirname(sys\.argv\[0\])|"${PREFIX}/libexec"|g' \ ${WRKSRC}/pkundu/meica.py ${REINPLACE_CMD} \ -e 's|g_info|afni_g_info|g' \ ${WRKSRC}/rickr/Dimon.c \ ${WRKSRC}/rickr/Dimon1.c \ ${WRKSRC}/afni_history_rickr.c \ ${WRKSRC}/mri_dicom_stuff.c \ ${WRKSRC}/mri_process_siemens.c \ ${WRKSRC}/mri_read_dicom.c \ ${WRKSRC}/to3d.c \ ${WRKSRC}/mri_dicom_stuff.h post-build: ${MKDIR} ${PRESTAGE}/bin \ ${PRESTAGE}/scripts \ ${PRESTAGE}/lib \ ${PRESTAGE}/include \ ${PRESTAGE}/trash \ ${PRESTAGE}/doc \ ${PRESTAGE}/share ${MV} ${INSTALL_WRKSRC}/libf2c.a \ ${PRESTAGE}/trash ${MV} ${INSTALL_WRKSRC}/*.a \ ${INSTALL_WRKSRC}/*.so \ ${PRESTAGE}/lib ${MV} ${INSTALL_WRKSRC}/funstuff \ ${INSTALL_WRKSRC}/AFNI.*rc \ ${INSTALL_WRKSRC}/afnigui* \ ${PRESTAGE}/share ${MV} ${INSTALL_WRKSRC}/*.h \ ${PRESTAGE}/include ${MV} ${INSTALL_WRKSRC}/README* \ ${PRESTAGE}/doc for binary in `${FILE} ${INSTALL_WRKSRC}/* | fgrep 'ELF' | ${AWK} -F ':' ' { print $$1 }'` ; do \ ${MV} $${binary} ${PRESTAGE}/bin ; \ done ${MV} ${INSTALL_WRKSRC}/* \ ${PRESTAGE}/scripts ${MV} ${PRESTAGE}/scripts/meica.libs ${PRESTAGE} do-install: ${MKDIR} ${STAGEDIR}${DATADIR} \ ${STAGEDIR}${PREFIX}/lib/afni \ ${STAGEDIR}${PREFIX}/include/afni for f in ${PRESTAGE}/lib/*; do \ ${STRIP_CMD} $${f}; \ done ${INSTALL_DATA} ${PRESTAGE}/lib/* ${STAGEDIR}${PREFIX}/lib/afni ${INSTALL_DATA} ${PRESTAGE}/include/* ${STAGEDIR}${PREFIX}/include/afni cd ${PRESTAGE}/share && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR} ${INSTALL_PROGRAM} ${PRESTAGE}/bin/* ${STAGEDIR}${PREFIX}/bin ${INSTALL_SCRIPT} ${PRESTAGE}/scripts/* ${STAGEDIR}${PREFIX}/bin cd ${PRESTAGE} && ${COPYTREE_BIN} meica.libs \ ${STAGEDIR}${PREFIX}/libexec ${INSTALL_DATA} ${WRKSRC}/Atlases/* ${STAGEDIR}${DATADIR} ${INSTALL_MAN} ${WRKSRC}/afni.1 ${STAGEDIR}${MAN1PREFIX}/man/man1 ${MKDIR} ${STAGEDIR}${DOCSDIR} ${STAGEDIR}${PREFIX}/etc/mri ${INSTALL_DATA} ${PRESTAGE}/doc/* ${STAGEDIR}${DOCSDIR} ${INSTALL_SCRIPT} ${WRKDIR}/afni.cshrc ${WRKDIR}/afni.profile \ ${STAGEDIR}${PREFIX}/etc/mri .include Index: head/science/dlpoly-classic/Makefile =================================================================== --- head/science/dlpoly-classic/Makefile (revision 460451) +++ head/science/dlpoly-classic/Makefile (revision 460452) @@ -1,68 +1,67 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= dlpoly PORTVERSION= 1.8 PORTREVISION= 13 CATEGORIES= science java MASTER_SITES= http://ccpforge.cse.rl.ac.uk/gf/download/frsrelease/238/2028/ PKGNAMESUFFIX= classic DISTNAME= dl_class_${PORTVERSION} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Molecular dynamics simulation package BUILD_DEPENDS= ${LOCALBASE}/mpi/openmpi/bin/mpif90:net/openmpi RUN_DEPENDS= ${LOCALBASE}/mpi/openmpi/bin/mpirun:net/openmpi OPTIONS_DEFINE= GUI DOCS EXAMPLES OPTIONS_DEFAULT= GUI GUI_DESC= Install Java GUI USES= fortran gmake SUB_FILES= dlpoly-gui BUILD_WRKSRC= ${WRKSRC}/source MPIF90= ${LOCALBASE}/mpi/openmpi/bin/mpif90 GUI_USE= JAVA=yes GUI_PLIST_FILES= bin/dlpoly-gui \ ${DATADIR_REL}/GUI.jar post-patch: ${CP} ${WRKSRC}/build/MakePAR ${WRKSRC}/build/MakeSEQ ${BUILD_WRKSRC} ${REINPLACE_CMD} 's|gfortran|${FC}|g' ${BUILD_WRKSRC}/MakeSEQ ${REINPLACE_CMD} 's|DLPOLY\.X|dlpoly-classic|g' ${BUILD_WRKSRC}/MakeSEQ ${REINPLACE_CMD} 's|mpif90|${MPIF90}|g' \ ${BUILD_WRKSRC}/MakePAR ${REINPLACE_CMD} 's|DLPOLY\.X|dlpoly-classic-mpi|g' \ ${BUILD_WRKSRC}/MakePAR do-build: (cd ${BUILD_WRKSRC} && \ ${CP} -f MakeSEQ Makefile && \ ${MAKE} ${FC}) (cd ${BUILD_WRKSRC} && \ ${MAKE} clean && \ ${CP} -f MakePAR Makefile && \ ${MAKE} gfortran) .include do-install: ${INSTALL_PROGRAM} ${WRKSRC}/execute/dlpoly-classic ${STAGEDIR}${PREFIX}/bin ${INSTALL_PROGRAM} ${WRKSRC}/execute/dlpoly-classic-mpi ${STAGEDIR}${PREFIX}/bin @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/manual/* ${STAGEDIR}${DOCSDIR} @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${CP} -R ${WRKSRC}/execute ${STAGEDIR}${EXAMPLESDIR} ${RM} ${STAGEDIR}${EXAMPLESDIR}/execute/dlpoly* .if ${PORT_OPTIONS:MGUI} @${MKDIR} ${STAGEDIR}${DATADIR} ${INSTALL_DATA} ${WRKSRC}/java/GUI.jar ${STAGEDIR}${DATADIR} ${INSTALL_SCRIPT} ${WRKDIR}/dlpoly-gui ${STAGEDIR}${PREFIX}/bin .endif .include Index: head/science/fvcom/Makefile =================================================================== --- head/science/fvcom/Makefile (revision 460451) +++ head/science/fvcom/Makefile (revision 460452) @@ -1,56 +1,55 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= fvcom PORTVERSION= 2.7.1 PORTREVISION?= 10 CATEGORIES= science MASTER_SITES= http://fvcom.smast.umassd.edu/FVCOM/index.html/ DISTNAME= sourcecode1 DIST_SUBDIR= fvcom -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Unstructured Grid Finite Volume Coastal Ocean Model # Check netcdf lib for Fortran support! LIB_DEPENDS+= libnetcdff.so:science/netcdf-fortran \ liblapack.so:math/lapack \ libblas.so:math/lapack USES= fortran USE_GCC= yes WRKSRC= ${WRKDIR}/FVCOM2.7.1/FVCOM_source PLIST_FILES= ${MPIPREFIX}bin/${PORTNAME}${PKGNAMESUFFIX} RESTRICTED= Requires (free) registration .include .if !exists(${DISTDIR}/${DIST_SUBDIR}/${DISTFILES}) IGNORE= may not be redistributed because of licensing reasons.\ Please register at http://fvcom.smast.umassd.edu/FVCOM/index.html\ in order to download the source code ${DISTFILES}\ and place it in ${DISTDIR}/${DIST_SUBDIR}/ .endif MAKE_JOBS_UNSAFE= yes post-extract: ${MV} ${WRKSRC}/makefile ${WRKSRC}/Makefile post-patch: ${REINPLACE_CMD} -e 's|gcc|${CC}|g' \ ${WRKDIR}/FVCOM2.7.1/METIS_source/makefile ${REINPLACE_CMD} -e 's|cpp|${CPP}|g' \ ${WRKDIR}/FVCOM2.7.1/FVCOM_source/Makefile pre-build: (cd ${WRKSRC}/../METIS_source && make) do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/${MPIPREFIX}bin ${INSTALL_PROGRAM} ${WRKSRC}/fvcom \ ${STAGEDIR}${PREFIX}/${MPIPREFIX}bin/${PORTNAME}${PKGNAMESUFFIX} .include Index: head/science/fvcom-mpi/Makefile =================================================================== --- head/science/fvcom-mpi/Makefile (revision 460451) +++ head/science/fvcom-mpi/Makefile (revision 460452) @@ -1,18 +1,17 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTREVISION= 10 PKGNAMESUFFIX= -openmpi MPIPREFIX= mpi/openmpi/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org LIB_DEPENDS+= libmpi.so:net/openmpi MASTERDIR= ${.CURDIR}/../fvcom MAKE_ARGS+= FC=${LOCALBASE}/${MPIPREFIX}bin/mpif90 \ PORT_CPP_FLAGS+=-DMULTIPROCESSOR .include "${MASTERDIR}/Makefile" Index: head/science/nifticlib/Makefile =================================================================== --- head/science/nifticlib/Makefile (revision 460451) +++ head/science/nifticlib/Makefile (revision 460452) @@ -1,29 +1,28 @@ -# Created by: Jason W. Bacon # $FreeBSD$ PORTNAME= nifticlib PORTVERSION= 2.0.0 PORTREVISION= 1 CATEGORIES= science graphics MASTER_SITES= SF/niftilib/nifticlib/nifticlib_2_0_0 -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Neuroimaging Informatics Technology Initiative data format LICENSE= PD USES= gmake # AFNI currently has nifti embedded in the distfile and installs the # nifti bins by itself. CONFLICTS= afni-[0-9]* dbh-[0-9]* CFLAGS+= -fPIC do-install: ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin ${INSTALL_DATA} ${WRKSRC}/lib/*.a ${STAGEDIR}${PREFIX}/lib ${INSTALL_DATA} ${WRKSRC}/include/*.h ${STAGEDIR}${PREFIX}/include ${INSTALL_MAN} ${FILESDIR}/nifticlib.1 ${STAGEDIR}${MANPREFIX}/man/man1 .include Index: head/science/openkim/Makefile =================================================================== --- head/science/openkim/Makefile (revision 460451) +++ head/science/openkim/Makefile (revision 460452) @@ -1,51 +1,50 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= openkim PORTVERSION= 1.1.1 PORTREVISION= 5 CATEGORIES= science MASTER_SITES= http://s3.openkim.org/openkim-api/ DISTNAME= ${PORTNAME}-api-v${PORTVERSION} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Knowledgebase of Interatomic Models LICENSE= CDDL MAKE_ENV+= KIM_DIR=${WRKSRC} USES= gmake fortran tar:tgz MAKE_JOBS_UNSAFE=yes .include # Is there a better way to detect 32-bit systems? .if ${ARCH} == armv6 || ${ARCH} == armv7 || ${ARCH} == i386 || ${ARCH} == mips || ${ARCH} == powerpc MAKE_ENV+= KIM_SYSTEM32="yes" .endif post-patch: ${REINPLACE_CMD} \ -e "s|gcc|${CC}|g" \ -e "s|g++|${CXX}|g" \ -e "s|= gfortran|= ${FC}|g" \ -e "s|-O3|${CFLAGS}|g" \ -e "s|LINKLIBFLAG =|LINKLIBFLAG = ${LDFLAGS}|" \ ${WRKSRC}/KIM_API/GNU_compiler_settings.mk # Required for main build to succeed pre-build: (cd ${WRKSRC} && ${MAKE_CMD} KIM_DIR=${WRKSRC} examples) do-install: ${MKDIR} ${STAGEDIR}${PREFIX}/lib ${STAGEDIR}${PREFIX}/include/KIM_API ${INSTALL_DATA} ${WRKSRC}/KIM_API/libkim.a ${STAGEDIR}${PREFIX}/lib ${INSTALL_DATA} ${WRKSRC}/KIM_API/*.h ${STAGEDIR}${PREFIX}/include/KIM_API regression-test: (cd ${WRKSRC}/TESTs/ex_test_Ar_free_cluster_CLUSTER_F90 && \ ${ECHO_CMD} "ex_model_Ar_P_MLJ_CLUSTER_C" | ./ex_test_Ar_free_cluster_CLUSTER_F90) .include Index: head/science/voro++/Makefile =================================================================== --- head/science/voro++/Makefile (revision 460451) +++ head/science/voro++/Makefile (revision 460452) @@ -1,30 +1,29 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= voro++ PORTVERSION= 0.4.6 CATEGORIES= science MASTER_SITES= http://math.lbl.gov/voro++/download/dir/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Three-dimensional computations of the Voronoi tessellation LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE USES= gmake post-patch: ${REINPLACE_CMD} \ -e 's|CXX=|CXX?=|g' \ -e 's|CFLAGS=|CFLAGS?=|g' \ -e 's|PREFIX=.*|PREFIX?=|g' \ ${WRKSRC}/config.mk ${REINPLACE_CMD} \ -e 's|$$(PREFIX)|$$(DESTDIR)$$(PREFIX)|g' \ ${WRKSRC}/Makefile post-install: ${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/voro++ .include Index: head/sysutils/condor/Makefile =================================================================== --- head/sysutils/condor/Makefile (revision 460451) +++ head/sysutils/condor/Makefile (revision 460452) @@ -1,88 +1,88 @@ # Created by: Andy Pavlo # $FreeBSD$ # # Note: Make sure there are no older versions of HTCondor installed during # build. The build system may pick up incompatible headers and libs. PORTNAME= condor PORTVERSION= 8.4.9 PORTREVISION= 7 CATEGORIES= sysutils net MASTER_SITES= http://www.acadix.biz/Ports/distfiles/ DISTNAME= condor_src-${PORTVERSION}-all-all -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= High-throughput computing on distributively owned resources LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE-2.0.txt LIB_DEPENDS+= libkrb5support.so:security/krb5 \ libpcre.so:devel/pcre \ libcurl.so:ftp/curl \ libboost_python.so:devel/boost-python-libs \ libexpat.so:textproc/expat2 WRKSRC= ${WRKDIR}/condor-${PORTVERSION} USE_LDCONFIG= yes # Does not build with Python 3 USES= cmake cpe perl5 pgsql python:2 shebangfix ssl CPE_VENDOR= condor_project SHEBANG_FILES= src/condor_scripts/condor_qsub \ src/condor_gridmanager/remote_gahp \ src/condor_examples/condor_limits_wrapper.sh \ src/condor_examples/condor_schedd.init \ src/condor_starter.V6.1/condor_ssh_to_job_shell_setup \ src/condor_job_router/condor_router_history WANT_PGSQL= server CXXFLAGS+= -I${LOCALBASE}/include -fPIC LDFLAGS+= -Wl,-rpath=${_GCC_RUNTIME}:${LOCALBASE}/lib:/usr/lib:/lib -fPIC # Does not build with Python 3 CMAKE_ARGS+= -DCMAKE_CXX_FLAGS:STRING=${CXXFLAGS} \ -DCMAKE_EXE_LINKER_FLAGS:STRING=${LDFLAGS} \ -DPYTHON_INCLUDE_DIR:PATH=${LOCALBASE}/include/${PYTHON_VERSION} \ -DPYTHON_LIBRARY:FILEPATH=${LOCALBASE}/lib/lib${PYTHON_VERSION}.so SUB_FILES= condor-config condor_config.local pkg-message PLIST_SUB+= CONDOR_UVER=${PORTVERSION:S/./_/g} USERS= condor GROUPS= ${USERS} USE_RC_SUBR= condor PORTEXAMPLES= * PORTDOCS= * OPTIONS_DEFINE= DOCS EXAMPLES pre-everything:: @( ${PRINTF} "\nWARNING: Condor needs approximately 3GB to build!"; \ ${PRINTF} " Please make sure your build environment has that much before continuing.\n" ) post-patch: @${REINPLACE_CMD} \ -e 's,\(set( C_SHARE_EXAMPLES \)share/condor,\1${EXAMPLESDIR_REL},' \ ${WRKSRC}/build/cmake/CondorPackageConfig.cmake @${REINPLACE_CMD} \ -e '/create_symlink/d' \ ${WRKSRC}/src/condor_scripts/CMakeLists.txt @${REINPLACE_CMD} \ -e 's|/usr/local/condor|${PREFIX}|g' \ -e 's|$$(LOCAL_DIR)/condor_config.local|$$(RELEASE_DIR)/etc/condor_config.local|g' \ -e 's|/bin/mail|/usr/bin/mail|g' \ -e 's|/usr/bin/java|${LOCALBASE}/bin/java|g' \ -e 's|^CONDOR_HOST|## CONDOR_HOST|' \ -e 's|#CONDOR_IDS=x.x|CONDOR_IDS=466.466|' \ ${WRKSRC}/src/condor_examples/condor_config.annotated post-install: ${INSTALL_DATA} \ ${STAGEDIR}${ETCDIR}/examples/condor_config.annotated \ ${STAGEDIR}${PREFIX}/etc/condor_config.sample ${INSTALL_DATA} ${WRKDIR}/condor_config.local \ ${STAGEDIR}${PREFIX}/etc/condor_config.local.sample ${INSTALL_SCRIPT} ${WRKDIR}/condor-config ${STAGEDIR}${PREFIX}/sbin .include Index: head/sysutils/desktop-installer/Makefile =================================================================== --- head/sysutils/desktop-installer/Makefile (revision 460451) +++ head/sysutils/desktop-installer/Makefile (revision 460452) @@ -1,30 +1,29 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= desktop-installer DISTVERSION= 0.6.0 CATEGORIES= sysutils MASTER_SITES= http://acadix.biz/Ports/distfiles/ MAINTAINER= jwb@FreeBSD.org COMMENT= Quickly configure a FreeBSD desktop system LICENSE= BSD2CLAUSE RUN_DEPENDS= auto-admin>=0.4.2:sysutils/auto-admin USES= tar:xz NO_BUILD= yes NO_ARCH= yes do-install: ${INSTALL_SCRIPT} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/sbin ${INSTALL_MAN} ${WRKSRC}/Doc/${PORTNAME}.man \ ${STAGEDIR}${PREFIX}/man/man1/${PORTNAME}.1 ${MKDIR} ${STAGEDIR}${DATADIR} cd ${WRKSRC}/Data && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR} ${MKDIR} ${STAGEDIR}${DATADIR}/Scripts ${INSTALL_SCRIPT} ${WRKSRC}/Scripts/* ${STAGEDIR}${DATADIR}/Scripts .include Index: head/sysutils/diskimage-tools/Makefile =================================================================== --- head/sysutils/diskimage-tools/Makefile (revision 460451) +++ head/sysutils/diskimage-tools/Makefile (revision 460452) @@ -1,26 +1,25 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= diskimage-tools PORTVERSION= 0.1 CATEGORIES= sysutils MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Convenience tools for manipulating disk images LICENSE= BSD NO_BUILD= yes USES= tar:xz do-install: @${MKDIR} ${STAGEDIR}${PREFIX}/sbin ${INSTALL_SCRIPT} ${WRKSRC}/mount_cd9660_image \ ${WRKSRC}/umount_cd9660_image ${WRKSRC}/img2dev \ ${STAGEDIR}${PREFIX}/sbin ${INSTALL_MAN} ${WRKSRC}/mount_cd9660_image.1 \ ${WRKSRC}/umount_cd9660_image.1 ${WRKSRC}/img2dev.1 \ ${STAGEDIR}${MANPREFIX}/man/man1 .include Index: head/sysutils/endian/Makefile =================================================================== --- head/sysutils/endian/Makefile (revision 460451) +++ head/sysutils/endian/Makefile (revision 460452) @@ -1,20 +1,19 @@ -# Created by: Jason W. Bacon # $FreeBSD$ PORTNAME= endian PORTVERSION= 1.1 CATEGORIES= sysutils MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Report endianness of a system LICENSE= BSD2CLAUSE USES= tar:xz PLIST_FILES= bin/endian man/man1/endian.1.gz MAKE_ARGS= STAGEDIR=${STAGEDIR} .include Index: head/sysutils/ganglia-monitor-core/Makefile =================================================================== --- head/sysutils/ganglia-monitor-core/Makefile (revision 460451) +++ head/sysutils/ganglia-monitor-core/Makefile (revision 460452) @@ -1,114 +1,114 @@ # $FreeBSD$ PORTNAME= monitor-core PORTVERSION= 3.7.1 CATEGORIES= sysutils net MASTER_SITES= SF/ganglia/ganglia%20monitoring%20core/${PORTVERSION} PKGNAMEPREFIX= ganglia- .if defined(CLUSTER) PKGNAMESUFFIX= -${CLUSTER} .endif DISTNAME= ganglia-${PORTVERSION} -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Ganglia cluster monitor, monitoring daemon LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libapr-1.so:devel/apr1 \ libconfuse.so:devel/libconfuse \ libpcre.so:devel/pcre \ libexpat.so:textproc/expat2 OPTIONS_DEFINE= GMETAD OPTIONS_DEFAULT= GMETAD GMETAD_DESC= include gmetad USES= libtool pkgconfig python:2.7 GNU_CONFIGURE= yes CONFIGURE_ARGS= --enable-setuid=ganglia --enable-setgid=ganglia \ --with-python=${PYTHON_CMD} CONFIGURE_ENV= GANGLIA_ACK_SYSCONFDIR=1 CFLAGS+= -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib USERS= ganglia GROUPS= ganglia PLIST_SUB+= PORTVERSION=${PORTVERSION} SUB_FILES+= pkg-message INSTALL_TARGET= install-strip USE_RC_SUBR= gmond .include .if ${PORT_OPTIONS:MGMETAD} USE_RC_SUBR+= gmetad LIB_DEPENDS+= librrd.so:databases/rrdtool CONFIGURE_ARGS+= --with-gmetad PLIST_SUB+= GMETAD="" SUB_LIST+= GMETAD="" .else PLIST_SUB+= GMETAD="@comment " SUB_LIST+= GMETAD="\#" .endif USE_LDCONFIG= yes CONF_DIR= ${PREFIX}/etc MODULES= modcpu.so \ moddisk.so \ modload.so \ modmem.so \ modmulticpu.so \ modnet.so \ modproc.so \ modpython.so \ modsys.so # gmond.conf.5 and gmond.conf.html can be generated from conf.pod, but # doing so requires perl installed in the build stage. post-patch: ${REINPLACE_CMD} \ -e "s|/etc/ganglia/\(gm[a-z]*d.conf\)|${PREFIX}/etc/\1|g" \ ${WRKSRC}/README \ ${WRKSRC}/mans/gmetad.1 \ ${WRKSRC}/mans/gmond.1 ${REINPLACE_CMD} -e "s|nobody|ganglia|g" \ ${WRKSRC}/gmetad/gmetad.conf.in \ ${WRKSRC}/gmond/conf.pod \ ${WRKSRC}/gmond/gmond.conf.5 \ ${WRKSRC}/gmond/gmond.conf.html post-build: ${WRKSRC}/gmond/gmond -t > ${WRKDIR}/gmond.conf post-install: ${INSTALL_DATA} ${WRKDIR}/gmond.conf \ ${STAGEDIR}${PREFIX}/etc/gmond.conf.sample .if ${PORT_OPTIONS:MGMETAD} ${INSTALL_SCRIPT} ${FILESDIR}/gmetasnap.sh \ ${STAGEDIR}${PREFIX}/sbin/gmetasnap ${INSTALL_DATA} ${WRKSRC}/gmetad/gmetad.conf \ ${STAGEDIR}${PREFIX}/etc/gmetad.conf.sample ${INSTALL_MAN} ${WRKSRC}/mans/gmetad.1 \ ${STAGEDIR}${MANPREFIX}/man/man1 .endif ${INSTALL_MAN} \ ${WRKSRC}/mans/gmetric.1 \ ${WRKSRC}/mans/gmond.1 \ ${WRKSRC}/mans/gstat.1 \ ${STAGEDIR}${MANPREFIX}/man/man1 ${INSTALL_MAN} ${WRKSRC}/gmond/gmond.conf.5 \ ${STAGEDIR}${MANPREFIX}/man/man5 ${MKDIR} ${STAGEDIR}/var/db/ganglia/rrds ${MKDIR} ${STAGEDIR}${PREFIX}/lib/ganglia/python_modules .include Index: head/sysutils/mcweject/Makefile =================================================================== --- head/sysutils/mcweject/Makefile (revision 460451) +++ head/sysutils/mcweject/Makefile (revision 460452) @@ -1,26 +1,25 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= mcweject PORTVERSION= 1.1 CATEGORIES= sysutils MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Removable media eject LICENSE= BSD3CLAUSE SUB_FILES= pkg-message CONFLICTS= eject-[0-9]* USES= tar:xz do-install: ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${WRKSRC}/eject.allow ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_PROGRAM} ${WRKSRC}/eject ${STAGEDIR}${PREFIX}/sbin ${INSTALL_MAN} ${WRKSRC}/eject.1 ${STAGEDIR}${PREFIX}/man/man1 .include Index: head/sysutils/parafly/Makefile =================================================================== --- head/sysutils/parafly/Makefile (revision 460451) +++ head/sysutils/parafly/Makefile (revision 460452) @@ -1,25 +1,24 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= parafly PORTVERSION= 2013.01.21 PORTREVISION= 3 CATEGORIES= sysutils MASTER_SITES= SF/${PORTNAME}/ DISTNAME= ${PORTNAME}-r2013-01-21 -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Process multiple commands in parallel on a single server LICENSE= BSD3CLAUSE USES= compiler:openmp tar:tgz GNU_CONFIGURE= yes CXXFLAGS+= -fopenmp LDFLAGS+= -fopenmp PLIST_FILES= bin/ParaFly .include Index: head/sysutils/slurm-wlm/Makefile =================================================================== --- head/sysutils/slurm-wlm/Makefile (revision 460451) +++ head/sysutils/slurm-wlm/Makefile (revision 460452) @@ -1,143 +1,142 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= slurm DISTVERSION= 17.02.9 PORTREVISION= 1 CATEGORIES= sysutils MASTER_SITES= http://www.schedmd.com/download/latest/ \ http://www.schedmd.com/download/archive/ \ http://www.schedmd.com/download/development/ PKGNAMESUFFIX= -wlm MAINTAINER= jrm@FreeBSD.org COMMENT= Simple Linux Utility for Resource Management LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/COPYING LIB_DEPENDS= libjson-c.so:devel/json-c \ libsysinfo.so:devel/libsysinfo \ libmunge.so:security/munge \ liblz4.so:archivers/liblz4 USERS= slurm GROUPS= ${USERS} USES= gmake libtool pkgconfig python:build readline:port shebangfix \ ssl tar:bz2 USE_LDCONFIG= yes USE_PERL5= configure USE_RC_SUBR= slurmctld slurmd GNU_CONFIGURE= yes INSTALL_TARGET= install-strip PLIST_SUB= PORTVERSION="${PORTVERSION}" SHEBANG_FILES= doc/html/shtml2html.py doc/man/man2html.py OPTIONS_DEFINE= CURL DOCS GTK2 HDF5 HWLOC IPMI MYSQL RRD LINUX OPTIONS_DEFAULT=HDF5 HWLOC OPTIONS_SUB= yes CURL_DESC= Require cURL for elasticsearch plugins GTK2_DESC= Build sview GUI config tool HDF5_DESC= Job profiling using HDF5 HWLOC_DESC= Portable hardware locality IPMI_DESC= IPMI energy consumption accounting RRD_DESC= RRD external sensor data collection LINUX_DESC= Support jobacct_gather/linux (requires linprocfs) DOCS_BUILD_DEPENDS= man2html:textproc/man2html CURL_LIB_DEPENDS= libcurl.so:ftp/curl CURL_CONFIGURE_WITH= libcurl GTK2_USE= GNOME=cairo,gdkpixbuf2,glib20,gtk20 GTK2_LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ libfreetype.so:print/freetype2 GTK2_USES= gettext # Neither of these work. See post-patch below. #GTK2_CONFIGURE_ENV_OFF= ac_gtk_test=no #GTK2_CONFIGURE_OFF= --disable-gtktest HDF5_LIB_DEPENDS= libhdf5.so:science/hdf5 \ libsz.so:science/szip HDF5_CONFIGURE_WITH= hdf5 HWLOC_LIB_DEPENDS= libhwloc.so:devel/hwloc HWLOC_CONFIGURE_WITH= hwloc IPMI_LIB_DEPENDS= libfreeipmi.so:sysutils/freeipmi IPMI_CONFIGURE_WITH= freeipmi MYSQL_USES= mysql MYSQL_CONFIGURE_with= mysql MYSQL_CONFIGURE_OFF= --with-mysql_config=/nonexistent RRD_LIB_DEPENDS= librrd.so:databases/rrdtool RRD_CONFIGURE_WITH= rrdtool LINUX_USES= linux CFLAGS+= -I${WRKSRC}/slurm -I${LOCALBASE}/include LDFLAGS+= -L${LOCALBASE}/lib -lsysinfo -lkvm # SLURM's configure enables interactive jobs if pty.h exists. Replacing # #include with appropriate headers will therefore not work, so instead # add a pty.h for the build. post-patch: @${CP} ${FILESDIR}/pty.h ${WRKSRC}/slurm @${REINPLACE_CMD} -e 's|sched_setaffinity|cpuset_setaffinity|g' \ ${WRKSRC}/configure @${REINPLACE_CMD} -e 's|/bin/mail|/usr/bin/mail|g' \ ${WRKSRC}/src/common/read_config.h \ ${WRKSRC}/contribs/seff/smail \ ${WRKSRC}/doc/html/configurator.easy.html.in \ ${WRKSRC}/doc/html/configurator.html.in \ ${WRKSRC}/contribs/cray/slurm.conf.template \ ${WRKSRC}/doc/man/man1/strigger.1 \ ${WRKSRC}/doc/man/man5/slurm.conf.5 @${REINPLACE_CMD} \ -e 's|=linux|=FreeBSD|g' \ -e 's|run/slurmctld.pid|run/slurm/slurmctld.pid|' \ -e 's|run/slurmd.pid|run/slurm/slurd.pid|' \ -e 's|SlurmdSpoolDir=.*|SlurmdSpoolDir=/var/spool/slurmd|' \ -e 's|StateSaveLocation=.*|StateSaveLocation=/var/run/slurm|' \ ${WRKSRC}/etc/slurm.conf.example post-patch-LINUX-on: @${REINPLACE_CMD} -e 's|"/proc|"/compat/linux/proc|g' \ ${WRKSRC}/src/slurmd/slurmstepd/req.c \ ${WRKSRC}/src/slurmd/slurmstepd/pdebug.c \ ${WRKSRC}/src/slurmd/slurmd/get_mach_stat.c \ ${WRKSRC}/src/slurmd/slurmd/read_proc.c \ ${WRKSRC}/src/slurmd/common/xcpuinfo.c \ ${WRKSRC}/src/slurmd/common/xcgroup.c \ ${WRKSRC}/src/slurmd/common/set_oomadj.c \ ${WRKSRC}/src/slurmd/common/proctrack.c \ ${WRKSRC}/src/common/callerid.c \ ${WRKSRC}/src/plugins/task/affinity/affinity.c \ ${WRKSRC}/src/plugins/acct_gather_energy/rapl/acct_gather_energy_rapl.c \ ${WRKSRC}/src/plugins/jobacct_gather/cgroup/jobacct_gather_cgroup.c \ ${WRKSRC}/src/plugins/jobacct_gather/common/common_jag.c \ ${WRKSRC}/src/plugins/jobacct_gather/linux/jobacct_gather_linux.c \ ${WRKSRC}/src/plugins/switch/cray/scaling.c \ ${WRKSRC}/src/plugins/proctrack/cray/proctrack_cray.c \ ${WRKSRC}/src/plugins/proctrack/cgroup/proctrack_cgroup.c \ ${WRKSRC}/src/plugins/proctrack/pgid/proctrack_pgid.c \ ${WRKSRC}/src/plugins/proctrack/linuxproc/kill_tree.c \ ${WRKSRC}/src/plugins/proctrack/lua/proctrack_lua.c \ ${WRKSRC}/src/plugins/acct_gather_filesystem/lustre/acct_gather_filesystem_lustre.c \ ${WRKSRC}/contribs/cray/pam_job.c \ ${WRKSRC}/contribs/lua/proctrack.lua # Hack around nonfunctional --disable-gtktest flag post-patch-GTK2-off: @${REINPLACE_CMD} -e 's|min_gtk_version=.*|min_gtk_version=2000.0.0|' \ ${WRKSRC}/configure post-install: ${INSTALL_DATA} ${WRKSRC}/etc/slurm.conf.example \ ${STAGEDIR}${PREFIX}/etc/slurm.conf.sample .include Index: head/textproc/xml-format/Makefile =================================================================== --- head/textproc/xml-format/Makefile (revision 460451) +++ head/textproc/xml-format/Makefile (revision 460452) @@ -1,20 +1,19 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= xml-format PORTVERSION= 0.2 CATEGORIES= textproc MASTER_SITES= http://acadix.biz/Ports/distfiles/ MAINTAINER= johans@FreeBSD.org COMMENT= XML beautifier MAKE_ENV+= DATADIR=${DATADIR} do-install: ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/${PORTNAME}.1 ${STAGEDIR}${PREFIX}/man/man1 ${MKDIR} ${STAGEDIR}${DATADIR} cd ${WRKSRC} && ${COPYTREE_SHARE} Config ${STAGEDIR}${DATADIR} .include Index: head/www/webbrowser/Makefile =================================================================== --- head/www/webbrowser/Makefile (revision 460451) +++ head/www/webbrowser/Makefile (revision 460452) @@ -1,23 +1,22 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= webbrowser PORTVERSION= 0.3 CATEGORIES= www MASTER_SITES= http://acadix.biz/Ports/distfiles/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Wrapper for running the "best" available WEB browser LICENSE= BSD2CLAUSE NO_BUILD= yes USES= tar:xz do-install: ${INSTALL_SCRIPT} ${WRKSRC}/webbrowser ${STAGEDIR}${PREFIX}/bin ${INSTALL_MAN} ${WRKSRC}/webbrowser.1 ${STAGEDIR}${MAN1PREFIX}/man/man1 PLIST_FILES= bin/webbrowser man/man1/webbrowser.1.gz .include Index: head/x11/qterminal/Makefile =================================================================== --- head/x11/qterminal/Makefile (revision 460451) +++ head/x11/qterminal/Makefile (revision 460452) @@ -1,25 +1,24 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= qterminal PORTVERSION= 0.8.0 CATEGORIES= x11 MASTER_SITES= LXQT MAINTAINER= jesper@schmitz.computer COMMENT= Lightweight Qt-based terminal emulator LICENSE= GPLv2 LIB_DEPENDS= libqtermwidget5.so:x11-toolkits/qtermwidget RUN_DEPENDS= liberation-fonts-ttf>=2.00:x11-fonts/liberation-fonts-ttf \ qterminal-l10n>0:x11/qterminal-l10n USES= cmake:outsource compiler:c++11-lang gettext-runtime \ localbase:ldflags lxqt pkgconfig tar:xz USE_QT5= buildtools_build core gui qmake_build dbus linguisttools \ widgets x11extras USE_XORG= x11 USE_LXQT= buildtools lxqt .include Index: head/x11-toolkits/qtermwidget/Makefile =================================================================== --- head/x11-toolkits/qtermwidget/Makefile (revision 460451) +++ head/x11-toolkits/qtermwidget/Makefile (revision 460452) @@ -1,21 +1,20 @@ -# Created by: Jason Bacon # $FreeBSD$ PORTNAME= qtermwidget PORTVERSION= 0.8.0 CATEGORIES= x11-toolkits MASTER_SITES= LXQT MAINTAINER= jesper@schmitz.computer COMMENT= Terminal widget for QTerminal LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE USES= cmake:outsource compiler:c++11-lang gettext-runtime lxqt \ pkgconfig tar:xz USE_LDCONFIG= yes USE_QT5= buildtools_build core gui qmake_build linguisttools widgets USE_LXQT= buildtools .include