diff --git a/biology/canu/Makefile b/biology/canu/Makefile index 868d364ced15..d9b670ebf467 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -1,68 +1,71 @@ PORTNAME= canu DISTVERSION= 2.2 -PORTREVISION= 2 +PORTREVISION= 3 CATEGORIES= biology java perl5 # Github auto-generated tarballs lack submodules MASTER_SITES= https://github.com/marbl/canu/releases/download/v${DISTVERSION}/ MAINTAINER= jwb@FreeBSD.org COMMENT= Single molecule sequence assembler WWW= https://canu.readthedocs.io/ LICENSE= GPLv2 LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL NOT_FOR_ARCHS= armv6 armv7 i386 mips powerpc powerpcspe NOT_FOR_ARCHS_REASON= Requires 64-bit processor LIB_DEPENDS= libboost_regex.so:devel/boost-libs RUN_DEPENDS= gnuplot:math/gnuplot USES= compiler:c++11-lang gmake localbase perl5 tar:xz USE_JAVA= yes JAVA_RUN= yes JAVA_VERSION= 8+ WRKSRC_SUBDIR= src # Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than # using a separate install target. MAKE_ENV= DESTDIR=${WRKSRC} CANU_BUILD_ENV=ports +CXXFLAGS+= -std=c++14 .include # Parasail should be unbundled, but that would be a project because it's # currently woven into the canu code post-extract: .if ${ARCH} == "aarch64" ${CP} ${FILESDIR}/cpuid_arm.c ${WRKSRC}/utility/src/parasail/cpuid.c .elif ${ARCH} == "powerpc64" || ${ARCH} == "powerpc64le" ${CP} ${FILESDIR}/cpuid_ppc.c ${WRKSRC}/utility/src/parasail/cpuid.c +.elif ${ARCH} != "amd64" + ${CP} ${FILESDIR}/cpuid_any.c ${WRKSRC}/utility/src/parasail/cpuid.c .endif pre-configure: @${REINPLACE_CMD} \ -e 's|-O4||g' \ -e 's|-funroll-loops||g' \ -e 's|-fexpensive-optimizations||g' \ ${WRKSRC}/Makefile @${REINPLACE_CMD} \ -e 's|RealBin/../lib/site_perl|RealBin/../${SITE_PERL_REL}/canu|g' \ ${WRKSRC}/pipelines/canu.pl # Upstream does not want to use lib/perl5/site_perl post-build: @${MKDIR} ${WRKSRC}/build/lib/perl5 ${MV} ${WRKSRC}/build/lib/site_perl ${WRKSRC}/build/lib/perl5 do-install: @${MKDIR} ${STAGEDIR}${PREFIX} (cd ${WRKSRC}/build && ${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX}) # STRIP_CMD fails without this under poudriere @${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/* @${STRIP_CMD} \ `file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1` (cd ${WRKSRC}/build && \ ${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX}) .include diff --git a/biology/canu/files/cpuid_any.c b/biology/canu/files/cpuid_any.c new file mode 100644 index 000000000000..be03bd4a479b --- /dev/null +++ b/biology/canu/files/cpuid_any.c @@ -0,0 +1,52 @@ +/** + * @file + * + * @author jeffrey.daily@gmail.com + * + * Copyright (c) 2015 Battelle Memorial Institute. + * + * For non-intel platforms, stub out the intel feature tests. + */ +#include "config.h" + +#include "parasail/cpuid.h" + +int parasail_can_use_avx512vbmi() +{ + return 0; +} + +int parasail_can_use_avx512bw() +{ + return 0; +} + +int parasail_can_use_avx512f() +{ + return 0; +} + +int parasail_can_use_avx2() +{ + return 0; +} + +int parasail_can_use_sse41() +{ + return 0; +} + +int parasail_can_use_sse2() +{ + return 0; +} + +int parasail_can_use_altivec() +{ + return 0; +} + +int parasail_can_use_neon() +{ + return 0; +} diff --git a/biology/canu/files/patch-utility_src_parasail_internal__sse.h b/biology/canu/files/patch-utility_src_parasail_internal__sse.h deleted file mode 100644 index ea03b5ab917c..000000000000 --- a/biology/canu/files/patch-utility_src_parasail_internal__sse.h +++ /dev/null @@ -1,12 +0,0 @@ ---- utility/src/parasail/internal_sse.h.orig 2021-12-17 22:10:09 UTC -+++ utility/src/parasail/internal_sse.h -@@ -10,7 +10,8 @@ - - #include - --#include -+#define SIMDE_ENABLE_NATIVE_ALIASES -+#include - - #include "parasail.h" - diff --git a/biology/canu/files/patch-utility_src_utility_align-ssw.H b/biology/canu/files/patch-utility_src_utility_align-ssw.H deleted file mode 100644 index 8da82c2d106a..000000000000 --- a/biology/canu/files/patch-utility_src_utility_align-ssw.H +++ /dev/null @@ -1,12 +0,0 @@ ---- utility/src/utility/align-ssw.H.orig 2021-12-17 22:12:23 UTC -+++ utility/src/utility/align-ssw.H -@@ -33,7 +33,8 @@ - #include - #include - #include --#include -+#define SIMDE_ENABLE_NATIVE_ALIASES -+#include - - - #define MAPSTR "MIDNSHP=X"