a9f015d155
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590
63 lines
2 KiB
Makefile
63 lines
2 KiB
Makefile
# $FreeBSD$
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PORTNAME= canu
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DISTVERSIONPREFIX= v
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DISTVERSION= 1.8
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PORTREVISION= 2
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CATEGORIES= biology java perl5
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Single molecule sequence assembler
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LICENSE= GPLv2
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LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
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BROKEN_aarch64= fails to link: undefined reference to omp_set_num_threads
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BROKEN_armv6= fails to install: mv: rename site_perl to /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv6/lib/perl5/site_perl: No such file or directory
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BROKEN_armv7= fails to install: mv: rename site_perl to /wrkdirs/usr/ports/biology/canu/work/canu-1.7/src/usr/local/FreeBSD-armv7/lib/perl5/site_perl: No such file or directory
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LIB_DEPENDS= libboost_regex.so:devel/boost-libs
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RUN_DEPENDS= gnuplot:math/gnuplot
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USES= compiler:openmp gmake perl5
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USE_JAVA= yes
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USE_GITHUB= yes
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JAVA_RUN= yes
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JAVA_VERSION= 1.8+
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GH_ACCOUNT= marbl
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WRKSRC_SUBDIR= src
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# Makefile compiles directly into ${DESTDIR}${PREFIX}
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MAKE_ENV+= DESTDIR=${WRKSRC}
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post-patch:
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${REINPLACE_CMD} \
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-e 's|-O4||g' \
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-e 's|-funroll-loops||g' \
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-e 's|-fexpensive-optimizations||g' \
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-e 's|amd64|${ARCH}|g' \
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${WRKSRC}/Makefile
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${REINPLACE_CMD} -e 's|\\$$bin/mhap-|${JAVAJARDIR}/mhap-|g' \
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${WRKSRC}/pipelines/canu/OverlapMhap.pm
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${REINPLACE_CMD} -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
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${WRKSRC}/pipelines/canu.pl
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# Upstream does not want to use lib/perl5/site_perl
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post-build:
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@${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
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${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \
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${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
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do-install:
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@${MKDIR} ${STAGEDIR}${PREFIX}
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(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
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${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
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# STRIP_CMD fails without this on 11.1 under poudriere
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@${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/*
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${STRIP_CMD} \
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`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
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(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
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${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
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.include <bsd.port.mk>
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