diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile index 9f4072a59815..866362583846 100644 --- a/biology/abyss/Makefile +++ b/biology/abyss/Makefile @@ -1,52 +1,53 @@ PORTNAME= abyss -DISTVERSION= 2.3.9 +DISTVERSION= 2.3.10 CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler -WWW= https://www.bcgsc.ca/resources/software/abyss +WWW= https://www.bcgsc.ca/resources/software/abyss/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE BROKEN_i386= result of comparison of constant 18446744073709551615 with expression of type 'size_t', see https://github.com/bcgsc/abyss/issues/310 BUILD_DEPENDS= ${LOCALBASE}/include/boost/version.hpp:devel/boost-libs \ ghc:lang/ghc \ pandoc:textproc/hs-pandoc # pandoc is required just for one man page: abyss-sealer LIB_DEPENDS= libbtllib.so:biology/btllib \ libffi.so:devel/libffi \ libgmp.so:math/gmp \ libmpich.so:net/mpich # binaries aren't linked with libmpich.so for some reason RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake USES= autoreconf compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite USE_GITHUB= yes GH_ACCOUNT= bcgsc SHEBANG_FILES= bin/${PORTNAME}-* DataBase/abyss-db-txt SHEBANG_LANG= make make_OLD_CMD= /usr/bin/make make_CMD= ${PREFIX}/bin/gmake GNU_CONFIGURE= yes CONFIGURE_ARGS= --without-sparsehash # configure fails to find std::hash, reported to the ML: https://groups.google.com/forum/#!topic/trans-abyss/SZDBKR5bKxs -GNU_CONFIGURE_MANPREFIX= ${PREFIX}/share -TEST_TARGET= check # tests fail to compile, see https://github.com/bcgsc/abyss/issues/453 +TEST_TARGET= check -OPTIONS_DEFINE= DOCS +PORTSCOUT= limit:^[0-9\.]*$$ # to ignore alpha-numeric tags PORTDOCS= * -PORTSCOUT= limit:^[0-9\.]*$$ # to ignore alpha-numeric tags +OPTIONS_DEFINE= DOCS + +TESTING_UNSAFE= yes # tests fail to compile, see https://github.com/bcgsc/abyss/issues/453 .include .if ${OPSYS} == FreeBSD CFLAGS+= -Wno-error=unused-but-set-variable .endif .include diff --git a/biology/abyss/distinfo b/biology/abyss/distinfo index c57848eae017..9846a81f350c 100644 --- a/biology/abyss/distinfo +++ b/biology/abyss/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1726117023 -SHA256 (bcgsc-abyss-2.3.9_GH0.tar.gz) = 68e0bb05526a1daaeea91e036fb227e7adde938fa2eeaa7c7225997c00e367d5 -SIZE (bcgsc-abyss-2.3.9_GH0.tar.gz) = 1323783 +TIMESTAMP = 1730727252 +SHA256 (bcgsc-abyss-2.3.10_GH0.tar.gz) = 08ff30002113280ae75228eb1e29cf835318c7ef783ccf24fbe7350d49b4043c +SIZE (bcgsc-abyss-2.3.10_GH0.tar.gz) = 1323490